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Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to L-captopril
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG4000, Lithium Sulfate, Tris-Hydrochloride
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.097 α = 90 b = 68.097 β = 90 c = 49.11 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2015-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.02 50 99.6 64.2 11 16635
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 2.02 2.05 99.1 0.306 17.1 10.7
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 3VPE 2.02 50 15711 904 99.58 0.21354 0.2098 0.2165 0.28188 0.2839 RANDOM 40.209
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] -1.04 -0.52 -1.04 3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.031 r_dihedral_angle_4_deg 19.497 r_dihedral_angle_3_deg 15.436 r_long_range_B_other 8.335 r_long_range_B_refined 8.324 r_dihedral_angle_1_deg 8.204 r_scangle_other 6.256 r_mcangle_it 5.988 r_mcangle_other 5.988 r_mcbond_it 4.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.031 r_dihedral_angle_4_deg 19.497 r_dihedral_angle_3_deg 15.436 r_long_range_B_other 8.335 r_long_range_B_refined 8.324 r_dihedral_angle_1_deg 8.204 r_scangle_other 6.256 r_mcangle_it 5.988 r_mcangle_other 5.988 r_mcbond_it 4.833 r_mcbond_other 4.831 r_scbond_other 4.642 r_scbond_it 4.638 r_angle_refined_deg 1.12 r_angle_other_deg 0.648 r_chiral_restr 0.068 r_gen_planes_refined 0.012 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 1921 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing