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Crystal structure of metallo-beta-lactamase VMB-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 289 1.8 M Ammonium citrate tribasic pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.4 63.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.957 α = 90 b = 94.981 β = 90 c = 145.503 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 PILATUS3 6M 2018-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 50 99.2 0.181 17 12.9 143862
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 98.4 1.31 1.31 2.625 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.7 39.79 136108 7331 98.92 0.16771 0.16656 0.1796 0.18928 0.201 RANDOM 15.655
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] 0.07 0.09 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.638 r_dihedral_angle_3_deg 12.856 r_dihedral_angle_4_deg 9.14 r_dihedral_angle_1_deg 6.543 r_long_range_B_refined 5.023 r_long_range_B_other 4.966 r_scangle_other 4.231 r_scbond_it 2.798 r_scbond_other 2.789 r_mcangle_it 2.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.638 r_dihedral_angle_3_deg 12.856 r_dihedral_angle_4_deg 9.14 r_dihedral_angle_1_deg 6.543 r_long_range_B_refined 5.023 r_long_range_B_other 4.966 r_scangle_other 4.231 r_scbond_it 2.798 r_scbond_other 2.789 r_mcangle_it 2.214 r_mcangle_other 2.214 r_angle_refined_deg 1.695 r_angle_other_deg 1.505 r_mcbond_it 1.491 r_mcbond_other 1.478 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6810 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing