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Native VIM-7. Structural and computational investigations of VIM-7: Insights into the substrate specificity of VIM metallo-beta- lactamases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KO3 PDB ENTRY 1KO3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 22.5-23.5% POLYETHYLENE GLYCOL MONOMETHYL ETHERS (PEG MME) 2K, 0.1 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 5.0, 8 MM BETA-MERCAPTOETHANOL
Crystal Properties Matthews coefficient Solvent content 1.97 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.399 α = 90 b = 70.399 β = 90 c = 47.562 γ = 90
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 CCD 2010-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.86 29 97.4 0.06 14.9 5.8 19415 15.9
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 1.86 1.96 82.2 0.28 4 3.8
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 PDB ENTRY 1KO3 1.86 20 17386 1984 97.41 0.16531 0.16023 0.162 0.21011 0.2102 RANDOM 17.396
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] -0.03 -0.03 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.088 r_dihedral_angle_4_deg 16.306 r_dihedral_angle_3_deg 12.804 r_dihedral_angle_1_deg 6.784 r_scangle_it 4.721 r_scbond_it 2.782 r_mcangle_it 1.702 r_angle_refined_deg 1.685 r_mcbond_it 0.99 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.088 r_dihedral_angle_4_deg 16.306 r_dihedral_angle_3_deg 12.804 r_dihedral_angle_1_deg 6.784 r_scangle_it 4.721 r_scbond_it 2.782 r_mcangle_it 1.702 r_angle_refined_deg 1.685 r_mcbond_it 0.99 r_chiral_restr 0.127 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1705 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing