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Crystal structure of the metallo-beta-lactamase VIM-1 with 1649
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Experimentally determined structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 2.7M ammonium phosphate, 0.1M Tris, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.11 41.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.416 α = 90 b = 67.75 β = 93.49 c = 40.3 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M-F 2025-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.78380 Diamond I03
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 1.15 40.23 99.3 0.073 0.079 0.03 0.998 11.7 7 74363 11.64
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 1.15 1.17 98.2 0.953 1.045 0.421 0.684 5.9
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 FREE R-VALUE 1.15 40.23 1.34 74330 7348 99 0.1415 0.14 0.1475 0.1702 0.1736 17.76
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 7.2989 f_angle_d 0.9867 f_chiral_restr 0.0883 f_plane_restr 0.0098 f_bond_d 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1730 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PHENIX refinement pointless data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction