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Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with JMV-4690 (Cpd 31)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M cacodylate, 0.2 M Na-acetate, 5 mM DTT, 26% PEG8000
Crystal Properties Matthews coefficient Solvent content 1.8 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.14 α = 90 b = 79 β = 90 c = 79.69 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2011-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8726 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 56.104 89 0.089 0.102 0.048 10 3.7 14141 14141
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 91.5 0.366 0.366 0.422 0.205 2.1 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KO3 1.95 34.07 13432 707 88.15 0.1775 0.1744 0.1841 0.2362 0.2398 RANDOM 21.723
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.281 r_dihedral_angle_4_deg 18.354 r_dihedral_angle_3_deg 14.205 r_dihedral_angle_1_deg 7.361 r_angle_refined_deg 1.723 r_angle_other_deg 1.292 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.281 r_dihedral_angle_4_deg 18.354 r_dihedral_angle_3_deg 14.205 r_dihedral_angle_1_deg 7.361 r_angle_refined_deg 1.723 r_angle_other_deg 1.292 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1728 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing