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Crystal structure of the metallo-beta-lactamase VIM-31 in its oxidized form at 1.88 A
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 VAPOR DIFFUSION 8.5 296 VIM-31 (12 mg/ml) 1:1 dilution with the condition 0.2 M lithium sulphate, 0.1 M Tris-HCl pH 8.5, 30 % PEG 4000, VAPOR DIFFUSION, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.07 40.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.02 α = 90 b = 80.13 β = 91.71 c = 77.639 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2012-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 40.06 97.2 0.044 20 3.8 33380 33380
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.96 81.9 0.157 0.157 7.7 3.7 4079
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 1.88 40.06 31694 1685 99.19 0.14985 0.14745 0.1548 0.19478 0.1996 RANDOM 19.318
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] 10.13 3.74 -8.73 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.609 r_dihedral_angle_4_deg 20.197 r_dihedral_angle_3_deg 12.35 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.077 r_angle_other_deg 0.82 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.609 r_dihedral_angle_4_deg 20.197 r_dihedral_angle_3_deg 12.35 r_dihedral_angle_1_deg 6.18 r_angle_refined_deg 1.077 r_angle_other_deg 0.82 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 r_bond_other_d 0.003 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_it r_mcbond_other r_mcangle_it r_scbond_it 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 3490 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 8
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling