I have calculated Mathews coefficient also, the probability shows five molecules in ASU. But it fails to convince my supervisor. On Mon, Dec 12, 2016 at 6:52 AM, wrote:

Compute Matthews coefficient. e.g. using http://www.ruppweb.org/mattprob/default.html

Oleg

-----Original Message----- From: "Sharan Karade" Sent: Sunday, December 11, 2016 6:05am To: [email protected] Subject: [phenixbb] Asymmetric unit content

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I have solved the structure in C121 space group, having five molecules in asymmetric unit, my supervisor have doubt about the fifth molecule becoz of poor density fit, if i delete the fifth molecule, there is a space for the molecule and crystal is not continuous, i calculated difference map from Phenix by deleting fifth molecule and got the Map showing presence of molecule. My supervisor want me to get SetMet data, but crystals are diffracting poor (7A). Is there any way to convince my guide.

advance thanks for valuable suggestions.

-- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

Oleg Borbulevych, Ph.D. Staff Scientist QuantumBio, Inc. 2790 W. College Ave. State College, PA 16801 E-mail: [email protected], [email protected] Linkedin Professional Profile: http://www.linkedin.com/pub/ oleg-borbulevych/22/454/b80

-- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

In addition (to Oleg's suggestion): compute Polder map too! Pavel On 12/12/16 22:52, [email protected] wrote:

Compute Matthews coefficient. e.g. using http://www.ruppweb.org/mattprob/default.html

Oleg

-----Original Message----- From: "Sharan Karade" Sent: Sunday, December 11, 2016 6:05am To: [email protected] Subject: [phenixbb] Asymmetric unit content

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] all,

I have solved the structure in C121 space group, having five molecules in asymmetric unit, my supervisor have doubt about the fifth molecule becoz of poor density fit, if i delete the fifth molecule, there is a space for the molecule and crystal is not continuous, i calculated difference map from Phenix by deleting fifth molecule and got the Map showing presence of molecule. My supervisor want me to get SetMet data, but crystals are diffracting poor (7A). Is there any way to convince my guide.

advance thanks for valuable suggestions.

Thank you for valuabla suggestions. I apologies for misleading information. I solved the structure at 2.8A (native) as powel got correctly.During data collection out of 50 2 crystals diffracted better dan 3A. But my guide want me to get setMet data, unfortuanately crystals poorely diffracting (7A) now which grown in same condition and also tried to play with condition to get better crystal but failed. Is there any way to prove that with data what i have. ? On Monday, December 12, 2016, Roger Rowlett wrote:

The Matthews coefficient is relatively efficient at distinguishing likely ASU content for N<=4. However, the probability distribution of the solvent content of protein crystals is broad enough that it is difficult to distinguish from the Matthews coefficient alone if an ASU has say, 4 or 6 (or 6 or 8) molecules in the ASU. Realistically, the Matthews coefficient is going to give you a range of likely possibilities. 1 vs. 2 is easy to distinguish. Not so 4 vs. 5 vs. 6.

Ultimately, you have to look at your MR solution and the molecule packing in the unit cell. Said packing should make chemical sense, and reveal highly symmetric solvent channels. A periodic "gap" in your crystal packing, supported by un-filled electron density, is a clue that something might be missing. At 7A resolution, I would suspect that the electron density clarity would not be terrific.

5 molecules in the ASU seems a bit odd to me. (4 or 6 seems more probable.) If it is 5 molecules, one of the molecules would have to be on a symmetry axis, completing a "symmetry" dimer, with two other dimers in the ASU? I've seen 6 molecules in the ASU in C2, with one tetramer and one half-tetramer on the symmetry axis. When solving that one, the Matthews Probability calculator insisted that there were 4 molecules in the ASU. Turned out to be 6. I initially placed 4 molecules in the ASU, and saw a clear crystal-packing gap for another dimer that would fit neatly next to the symmetry axis.

_______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346

tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [email protected]

On 12/12/2016 9:52 AM, [email protected] wrote:

...

Compute Matthews coefficient. e.g. using http://www.ruppweb.org/mattprob/default.html

Oleg

-----Original Message----- From: "Sharan Karade" Sent: Sunday, December 11, 2016 6:05am To: [email protected] Subject: [phenixbb] Asymmetric unit content

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] all,

I have solved the structure in C121 space group, having five molecules in asymmetric unit, my supervisor have doubt about the fifth molecule becoz of poor density fit, if i delete the fifth molecule, there is a space for the molecule and crystal is not continuous, i calculated difference map from Phenix by deleting fifth molecule and got the Map showing presence of molecule. My supervisor want me to get SetMet data, but crystals are diffracting poor (7A). Is there any way to convince my guide.

advance thanks for valuable suggestions.

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

Dear, 7A could be sufficient to localise the Se-atoms from an anomalous difference map, when the data are collected at or beyond the peak wavelength, provided you can collect complete data. Since you seem to have the crystal, and if you have access to some synchrotron beamtime, go ahead and try. Best, Tim On Monday, December 12, 2016 7:42:37 AM CET Sharan Karade wrote:

Thank you for valuabla suggestions. I apologies for misleading information. I solved the structure at 2.8A (native) as powel got correctly.During data collection out of 50 2 crystals diffracted better dan 3A. But my guide want me to get setMet data, unfortuanately crystals poorely diffracting (7A) now which grown in same condition and also tried to play with condition to get better crystal but failed. Is there any way to prove that with data what i have. ?

On Monday, December 12, 2016, Roger Rowlett wrote:

...

The Matthews coefficient is relatively efficient at distinguishing likely ASU content for N<=4. However, the probability distribution of the solvent content of protein crystals is broad enough that it is difficult to distinguish from the Matthews coefficient alone if an ASU has say, 4 or 6 (or 6 or 8) molecules in the ASU. Realistically, the Matthews coefficient is going to give you a range of likely possibilities. 1 vs. 2 is easy to distinguish. Not so 4 vs. 5 vs. 6.

Ultimately, you have to look at your MR solution and the molecule packing in the unit cell. Said packing should make chemical sense, and reveal highly symmetric solvent channels. A periodic "gap" in your crystal packing, supported by un-filled electron density, is a clue that something might be missing. At 7A resolution, I would suspect that the electron density clarity would not be terrific.

5 molecules in the ASU seems a bit odd to me. (4 or 6 seems more probable.) If it is 5 molecules, one of the molecules would have to be on a symmetry axis, completing a "symmetry" dimer, with two other dimers in the ASU? I've seen 6 molecules in the ASU in C2, with one tetramer and one half-tetramer on the symmetry axis. When solving that one, the Matthews Probability calculator insisted that there were 4 molecules in the ASU. Turned out to be 6. I initially placed 4 molecules in the ASU, and saw a clear crystal-packing gap for another dimer that would fit neatly next to the symmetry axis.

_______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346

tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [email protected]

On 12/12/2016 9:52 AM, [email protected] wrote:

...

Compute Matthews coefficient. e.g. using http://www.ruppweb.org/mattprob/default.html

Oleg

-----Original Message----- From: "Sharan Karade" Sent: Sunday, December 11, 2016 6:05am To: [email protected] Subject: [phenixbb] Asymmetric unit content

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] all,

I have solved the structure in C121 space group, having five

molecules in asymmetric unit, my supervisor have doubt about the fifth molecule becoz of poor density fit, if i delete the fifth molecule, there is a space for the molecule and crystal is not continuous, i calculated difference map from Phenix by deleting fifth molecule and got the Map showing presence of molecule. My supervisor want me to get SetMet data, but crystals are diffracting poor (7A). Is there any way to convince my guide.

advance thanks for valuable suggestions.

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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