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Metal Beta-Lactamase VIM-2 in Complex with MBL inhibitor B9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 28% PEG3350,0.2 M Magnesium formate
Crystal Properties Matthews coefficient Solvent content 2.32 47.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.567 α = 90 b = 74.567 β = 90 c = 213.075 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 195 PIXEL DECTRIS PILATUS3 X CdTe 1M 2023-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.0 SSRF BL19U1
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 2.169 71.03 99.9 0.074 0.079 0.025 0.999 18.1 9.7 37418
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 2.17 2.29 99.9 1.041 1.097 0.343 0.955 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.169 35.568 1.36 37144 1993 99.38 0.2429 0.2388 0.2479 0.3142 0.3217
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.016 f_angle_d 1.439 f_chiral_restr 0.07 f_bond_d 0.023 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5199 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 84
Software Software Software Name Purpose PHENIX refinement Aimless data scaling HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction