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Crystal structure of the VIM-2 acquired metallo-beta-Lactamase in Complex with compound 8 (JMV-7207)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M cacodilate (pH 6.5), 5 mM DTT , 0.2 M Na-acetate, 26% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.33 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.967 α = 90 b = 78.069 β = 90 c = 79.114 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 EIGER2 XE 16M 2019-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979499 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.88 55.57 89.5 0.102 0.118 0.059 0.995 9.5 7.3 15310 25.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.98 99.4 0.814 0.953 0.49 0.712 2.3 7
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 6SP7 1.9 55.57 14566 743 89.65 0.1878 0.1841 0.1844 0.2633 0.2625 RANDOM 32.67
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] 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.972 r_dihedral_angle_4_deg 17.322 r_dihedral_angle_3_deg 16.291 r_dihedral_angle_1_deg 6.671 r_angle_refined_deg 1.439 r_chiral_restr 0.098 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1724 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing