Thank you for using RCSB. The following geometrical and stereochemical features have been calculated for your structure: CLOSE CONTACTS -------------- ==> Close contacts in same asymmetric unit. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Close contacts based on crystal symmetry. Distances smaller than 2.2 Angstroms are considered as close contacts. none BOND DISTANCES AND ANGLES ------------------------- ==> Bond and angle checks are performed by first computing the average rms error for all bonds and angles relative to standard values for nucleotide units [L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases, J.Am.Chem.Soc. 1996, 118, 509-518; A. Gelbin et al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J.Am.Chem.Soc. 1996, 118, 519-529] and amino acid units [R.A. Engh and R. Huber, Structure quality and target parameters, International Tables for Crystallography, Volume F, 2001, 382-392]. Any bond or angle which deviates from the dictionary values by more than six times this computed rms error is identified as an outlier. *** Covalent Bond Lengths: The overall RMS deviation for covalent bonds relative to the standard dictionary is 0.009 Angstroms All covalent bonds lie within a 6.0*RMSD range about the standard dictionary values. *** Covalent Angle Values: The overall RMS deviation for covalent angles relative to the standard dictionary is 1.3 degrees. The following table contains a list of the covalent bond angles greater than 6 times standard deviation. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Standard Name ID Number Angle Value Deviation ------------------------------------------------------------------------------------------- 1.8 DA K 2 N9 - C1' - O4' 110.1 108.3 0.3 2.5 DC K 4 N1 - C1' - O4' 110.8 108.3 0.3 -7.0 DT K 7 C1' - O4' - C4' 103.1 110.1 1.0 -4.8 DT K 8 N1 - C1' - O4' 103.2 108.0 0.7 -6.5 DT K 11 C1' - C2' - C3' 95.9 102.4 0.8 -8.2 DA K 13 C1' - C2' - C3' 94.2 102.4 0.8 1.8 DT L 2 N1 - C1' - O4' 110.1 108.3 0.3 -5.8 DT L 4 C1' - C2' - C3' 96.6 102.4 0.8 2.4 DT L 7 N1 - C1' - O4' 110.7 108.3 0.3 4.2 DT L 11 N3 - C4 - O4 124.1 119.9 0.6 -4.5 DG L 13 C2' - C3' - C4' 97.7 102.2 0.7 3.2 DG L 13 N9 - C1' - O4' 111.5 108.3 0.3 3.2 DT L 14 N1 - C1' - O4' 111.5 108.3 0.3 -4.9 DA C 2 C1' - C2' - C3' 97.5 102.4 0.8 3.1 DA C 2 N9 - C1' - O4' 111.4 108.3 0.3 2.3 DT C 5 N1 - C1' - O4' 110.6 108.3 0.3 3.9 DT C 7 N3 - C4 - O4 123.8 119.9 0.6 -4.7 DA C 10 N9 - C1' - O4' 103.3 108.0 0.7 -5.9 DT C 11 C1' - C2' - C3' 96.5 102.4 0.8 -5.2 DT C 11 C1' - C2' - C3' 97.2 102.4 0.8 3.4 DC D 3 N1 - C1' - O4' 111.7 108.3 0.3 2.5 DC D 3 N1 - C1' - O4' 110.8 108.3 0.3 -6.0 DT D 11 C1' - C2' - C3' 96.4 102.4 0.8 TORSION ANGLES -------------- The torsion angle distributions have been checked. Refer to the Procheck and/or Nucheck results on the RCSB Validation Report page. ==> The following table contains a list of torsion angles outside the expected Ramachandran regions [GJ. Kleywegt and TA. Jones, PHI/PSI-chology: Ramachandran Revisited, Structure 1996, 4, 1395 - 1400]. Residue Chain Sequence PSI PHI ILE I 8 84.88 -69.64 THR I 60 -130.67 -131.48 ILE J 8 85.60 -69.26 THR J 60 -147.81 -137.70 ASP J 61 105.13 -55.59 ILE A 8 85.40 -69.51 THR A 60 -147.07 -136.62 ASP A 61 106.93 -55.90 ILE B 8 85.12 -69.22 THR B 60 -129.39 -131.66 CHIRALITY --------- The chirality has been checked. O1P, O2P, and hydrogen atoms which do not follow the conventions defined by IUBMB (Liebecq, C. Compendium of Biochemical Nomenclature and Related Documents, 2nd ed.; Portland Press: London and Chapel Hill, 1992) and IUPAC (J.L. Markley, A. Bax, Y. Arata, C.W. Hilbers, R. Kaptein, B.D. Sykes, P.E. Wright and K. Wuthrich, Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids, Pure & Appl. Chem., Vol. 70, pp. 117-142, 1998) will be standardized at the time of processing; there is no need to change these labels in your coordinate file. Any other stereochemical violations are listed below. Chain Residue Residue Chiral Chiral Original Name Number Center Neighbor Atom Name ----- ------- ------- ------ -------- --------- K DA 3 P OP2 O2P K DA 3 P OP1 O1P K DC 4 P OP2 O2P K DC 4 P OP1 O1P K DT 5 P OP2 O2P K DT 5 P OP1 O1P K DA 6 P OP2 O2P K DA 6 P OP1 O1P K DT 7 P OP2 O2P K DT 7 P OP1 O1P K DT 8 P OP2 O2P K DT 8 P OP1 O1P K DT 9 P OP2 O2P K DT 9 P OP1 O1P K DA 10 P OP2 O2P K DA 10 P OP1 O1P K DT 11 P OP2 O2P K DT 11 P OP1 O1P K DA 12 P OP2 O2P K DA 12 P OP1 O1P K DA 13 P OP2 O2P K DA 13 P OP1 O1P K DG 14 P OP2 O2P K DG 14 P OP1 O1P L DC 3 P OP2 O2P L DC 3 P OP1 O1P L DT 4 P OP2 O2P L DT 4 P OP1 O1P L DT 5 P OP2 O2P L DT 5 P OP1 O1P L DA 6 P OP2 O2P L DA 6 P OP1 O1P L DT 7 P OP2 O2P L DT 7 P OP1 O1P L DA 8 P OP2 O2P L DA 8 P OP1 O1P L DA 9 P OP2 O2P L DA 9 P OP1 O1P L DT 11 P OP2 O2P L DT 11 P OP1 O1P L DA 12 P OP2 O2P L DA 12 P OP1 O1P L DG 13 P OP2 O2P L DG 13 P OP1 O1P L DT 14 P OP2 O2P L DT 14 P OP1 O1P C DA 3 P(A) OP2(A) O2P C DA 3 P(B) OP2(B) O2P C DA 3 P(A) OP1(A) O1P C DA 3 P(B) OP1(B) O1P C DC 4 P(A) OP2(A) O2P C DC 4 P(B) OP2(B) O2P C DC 4 P(A) OP1(A) O1P C DC 4 P(B) OP1(B) O1P C DT 5 P(A) OP2(A) O2P C DT 5 P(B) OP2(B) O2P C DT 5 P(A) OP1(A) O1P C DT 5 P(B) OP1(B) O1P C DA 6 P(A) OP2(A) O2P C DA 6 P(B) OP2(B) O2P C DA 6 P(A) OP1(A) O1P C DA 6 P(B) OP1(B) O1P C DT 7 P(A) OP2(A) O2P C DT 7 P(B) OP2(B) O2P C DT 7 P(A) OP1(A) O1P C DT 7 P(B) OP1(B) O1P C DT 8 P(A) OP2(A) O2P C DT 8 P(B) OP2(B) O2P C DT 8 P(A) OP1(A) O1P C DT 8 P(B) OP1(B) O1P C DT 9 P(A) OP2(A) O2P C DT 9 P(B) OP2(B) O2P C DT 9 P(A) OP1(A) O1P C DT 9 P(B) OP1(B) O1P C DA 10 P(A) OP2(A) O2P C DA 10 P(B) OP2(B) O2P C DA 10 P(A) OP1(A) O1P C DA 10 P(B) OP1(B) O1P C DT 11 P(A) OP2(A) O2P C DT 11 P(B) OP2(B) O2P C DT 11 P(A) OP1(A) O1P C DT 11 P(B) OP1(B) O1P C DA 12 P(A) OP2(A) O2P C DA 12 P(B) OP2(B) O2P C DA 12 P(A) OP1(A) O1P C DA 12 P(B) OP1(B) O1P C DA 13 P(A) OP2(A) O2P C DA 13 P(B) OP2(B) O2P C DA 13 P(A) OP1(A) O1P C DA 13 P(B) OP1(B) O1P C DG 14 P(A) OP2(A) O2P C DG 14 P(B) OP2(B) O2P C DG 14 P(A) OP1(A) O1P C DG 14 P(B) OP1(B) O1P D DC 3 P(A) OP2(A) O2P D DC 3 P(B) OP2(B) O2P D DC 3 P(A) OP1(A) O1P D DC 3 P(B) OP1(B) O1P D DT 4 P(A) OP2(A) O2P D DT 4 P(B) OP2(B) O2P D DT 4 P(A) OP1(A) O1P D DT 4 P(B) OP1(B) O1P D DT 5 P(A) OP2(A) O2P D DT 5 P(B) OP2(B) O2P D DT 5 P(A) OP1(A) O1P D DT 5 P(B) OP1(B) O1P D DA 6 P(A) OP2(A) O2P D DA 6 P(B) OP2(B) O2P D DA 6 P(A) OP1(A) O1P D DA 6 P(B) OP1(B) O1P D DT 7 P(A) OP2(A) O2P D DT 7 P(B) OP2(B) O2P D DT 7 P(A) OP1(A) O1P D DT 7 P(B) OP1(B) O1P D DA 8 P(A) OP2(A) O2P D DA 8 P(B) OP2(B) O2P D DA 8 P(A) OP1(A) O1P D DA 8 P(B) OP1(B) O1P D DA 9 P(A) OP2(A) O2P D DA 9 P(B) OP2(B) O2P D DA 9 P(A) OP1(A) O1P D DA 9 P(B) OP1(B) O1P D DT 11 P(A) OP2(A) O2P D DT 11 P(B) OP2(B) O2P D DT 11 P(A) OP1(A) O1P D DT 11 P(B) OP1(B) O1P D DA 12 P(A) OP2(A) O2P D DA 12 P(B) OP2(B) O2P D DA 12 P(A) OP1(A) O1P D DA 12 P(B) OP1(B) O1P D DG 13 P(A) OP2(A) O2P D DG 13 P(B) OP2(B) O2P D DG 13 P(A) OP1(A) O1P D DG 13 P(B) OP1(B) O1P D DT 14 P(A) OP2(A) O2P D DT 14 P(B) OP2(B) O2P D DT 14 P(A) OP1(A) O1P D DT 14 P(B) OP1(B) O1P SOLVENT ------- The following solvent molecules are further than 3.5 Angstroms away from macromolecule atoms in the asymmetric unit that are available for hydrogen bonding. Solvent molecules in extended hydration shells separated by 3.5 Angstroms or less are not listed. none The coordinates for water molecules which could be translated back into the asymmetric unit are listed. If you do not indicate otherwise we will replace the solvent coordinates in the entry with the ones below: