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Crystal Structure of the Di-Zinc Metallo-beta-lactamase VIM-4 from Pseudomonas aeruginosa
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 7 1.55 M AMMONIUM CITRATE TRIBASIC PH 7.0
Crystal Properties Matthews coefficient Solvent content 3.3 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.39 α = 90 b = 46.22 β = 105.24 c = 105.99 γ = 90
Symmetry Space Group C 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 CCD ADSC CCD 2008-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.9 47.3 98.6 0.1 8.92 3.6 52283 26.59
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 1.9 2 95.7 0.44 2.59 3.3
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 1.9 47.3 49667 2615 100 0.202 0.2 0.2046 0.254 0.2601 RANDOM 26.52
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] 1.67 -0.4 -1.02 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 16.411 r_sphericity_free 7.259 r_dihedral_angle_1_deg 6.337 r_sphericity_bonded 3.975 r_scangle_it 3.362 r_scbond_it 2.278 r_mcangle_it 1.579 r_rigid_bond_restr 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.772 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 16.411 r_sphericity_free 7.259 r_dihedral_angle_1_deg 6.337 r_sphericity_bonded 3.975 r_scangle_it 3.362 r_scbond_it 2.278 r_mcangle_it 1.579 r_rigid_bond_restr 1.48 r_angle_refined_deg 1.424 r_mcbond_it 1.023 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.231 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.099 r_metal_ion_refined 0.078 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3454 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing