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The structure of the metallo-beta-lactamase VIM-2 in complex with a triazolylthioacetamide 1b
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, HANGING DROP 295 20% PEG 8000, 0.1M MES, pH 6.5, 0.1M magnesium acetate
Crystal Properties Matthews coefficient Solvent content 1.87 34.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.759 α = 90 b = 79.421 β = 130.938 c = 67.981 γ = 90
Symmetry Space Group C 1 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 97 PIXEL DECTRIS PILATUS 6M 2017-12-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97852 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.775 39.1907632483 99.13 0.128 0.055 6.38 10 39958 16.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.775 1.839 99.13 0.14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1ko3 1.77521201035 39.1907632483 1.38229043876 39948 2019 99.1388509741 0.178080634821 0.176544854667 0.1773 0.206324845679 0.2084 25.9373964541
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 13.3134654622 f_angle_d 0.685664233573 f_chiral_restr 0.0495713551409 f_plane_restr 0.00398587243297 f_bond_d 0.0039252251841
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3486 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 84
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing