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Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Meropenem
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 4000, Lithium sulfate, Tris-Hydrochloride
Crystal Properties Matthews coefficient Solvent content 2.2 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.9 α = 107.95 b = 41.17 β = 102.46 c = 45.32 γ = 106.85
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 315r 2015-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AichiSR BEAMLINE BL2S1 1.12 AichiSR BL2S1
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 1.39 40.62 86.2 0.046 11.2 1.9 39458
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 1.39 1.47 86 0.063 1.9 1.9
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 1.39 40.62 37506 1947 86.16 0.13839 0.13705 0.1362 0.16313 0.1634 RANDOM 9.715
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] -0.09 0.55 -0.29 0.98 -0.41 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.446 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_3_deg 11.337 r_dihedral_angle_1_deg 7.01 r_long_range_B_refined 4.725 r_long_range_B_other 4.362 r_scangle_other 3.109 r_scbond_it 2.12 r_scbond_other 2.111 r_angle_refined_deg 1.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.446 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_3_deg 11.337 r_dihedral_angle_1_deg 7.01 r_long_range_B_refined 4.725 r_long_range_B_other 4.362 r_scangle_other 3.109 r_scbond_it 2.12 r_scbond_other 2.111 r_angle_refined_deg 1.562 r_mcangle_it 1.281 r_mcangle_other 1.281 r_mcbond_it 0.912 r_mcbond_other 0.909 r_angle_other_deg 0.766 r_chiral_restr 0.1 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 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 342 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing