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Crystal structure of the metallo-beta-lactamase VIM-1 with 1760
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
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.398 α = 90 b = 67.771 β = 93.17 c = 40.118 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 EIGER2 XE 16M 2025-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.78379 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.05 67.77 98.6 0.822 10.8 6.9 96446 9.53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.07 98.1 0.822
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 1.05 40.06 1.34 96395 9430 98.26 0.1134 0.1124 0.1224 0.1324 0.1385 14.92
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 12.8224 f_angle_d 1.2983 f_chiral_restr 0.0933 f_plane_restr 0.0124 f_bond_d 0.0111
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1728 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing