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Crystal structure of SMB-1 metallo-beta-lactamase in a complex with ASB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B1U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M lithium sulfate, 0.1M Tris-HCl (pH 8.5), 20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.997 α = 108.75 b = 41.682 β = 102.79 c = 45.66 γ = 105.86
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 S 6M 2018-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
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 1.17 50 93.1 0.041 37.3 3.5 73794
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.19 71.4 0.087 3.2
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 5B1U 1.17 33.5 70078 3714 93.68 0.13049 0.12941 0.1318 0.15053 0.154 RANDOM 10.12
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] 0.48 0.61 -0.32 0.82 -0.56 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.262 r_dihedral_angle_4_deg 18.268 r_dihedral_angle_3_deg 11.773 r_dihedral_angle_1_deg 7.038 r_long_range_B_refined 4.057 r_long_range_B_other 3.505 r_scangle_other 2.603 r_scbond_it 1.814 r_scbond_other 1.785 r_angle_refined_deg 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.262 r_dihedral_angle_4_deg 18.268 r_dihedral_angle_3_deg 11.773 r_dihedral_angle_1_deg 7.038 r_long_range_B_refined 4.057 r_long_range_B_other 3.505 r_scangle_other 2.603 r_scbond_it 1.814 r_scbond_other 1.785 r_angle_refined_deg 1.453 r_mcangle_other 1.207 r_mcangle_it 1.204 r_angle_other_deg 1.077 r_mcbond_it 0.876 r_mcbond_other 0.87 r_chiral_restr 0.302 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.001 r_bond_other_d 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 1932 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing