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Crystal structure of VMB-1 bound to hydrolyzed meropenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2 M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.108 α = 90 b = 96.777 β = 90 c = 131.716 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2019-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979191 SSRF BL17U
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 2.008 77.99 100 0.92 4.8 13.3 63155 32.08
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 2.01 2.12 100 0.87 2.3 13.8
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 6JV4 2.01 77.99 59946 3136 99.96 0.2118 0.2094 0.2175 0.2569 0.2627 RANDOM 35.999
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] -2.23 -0.65 2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.934 r_dihedral_angle_4_deg 19.082 r_dihedral_angle_3_deg 15.399 r_dihedral_angle_1_deg 7.045 r_angle_refined_deg 1.68 r_angle_other_deg 1.336 r_chiral_restr 0.256 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.934 r_dihedral_angle_4_deg 19.082 r_dihedral_angle_3_deg 15.399 r_dihedral_angle_1_deg 7.045 r_angle_refined_deg 1.68 r_angle_other_deg 1.336 r_chiral_restr 0.256 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6768 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction autoPROC data scaling PHASER phasing