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Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to 2-mercaptoethanesulfonate
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 PEG 6000, Lithium Chloride, MES
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.112 α = 90 b = 67.112 β = 90 c = 46.717 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 2012-02-19 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 2.1 58.13 100 42.5 11.6 13741
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 2.1 2.14 100 0.298 10.7 11.5
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 2.1 58.12 12964 763 99.99 0.15318 0.14967 0.1613 0.21437 0.22 RANDOM 22.88
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] -0.67 -0.34 -0.67 2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 18.736 r_dihedral_angle_3_deg 16.736 r_dihedral_angle_1_deg 8.088 r_long_range_B_refined 6.718 r_long_range_B_other 6.623 r_scangle_other 5.291 r_scbond_it 3.543 r_scbond_other 3.536 r_mcangle_it 3.467
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 18.736 r_dihedral_angle_3_deg 16.736 r_dihedral_angle_1_deg 8.088 r_long_range_B_refined 6.718 r_long_range_B_other 6.623 r_scangle_other 5.291 r_scbond_it 3.543 r_scbond_other 3.536 r_mcangle_it 3.467 r_mcangle_other 3.466 r_mcbond_it 2.489 r_mcbond_other 2.465 r_angle_refined_deg 1.163 r_angle_other_deg 0.683 r_chiral_restr 0.078 r_gen_planes_refined 0.013 r_bond_refined_d 0.009 r_gen_planes_other 0.003 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 183 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing