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Crystal Structure of the Mono-Zinc Metallo-beta-lactamase VIM-4 from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WHG PDB ENTRY 2WHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.55 M AMMONIUM CITRATE TRIBASIC PH 7.0 POWDER OF COMPOUND 18 IN THE DROP.
Crystal Properties Matthews coefficient Solvent content 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.13 α = 90 b = 45.67 β = 105.41 c = 105.03 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 2008-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.75 50 98.8 0.08 14.03 3.6 16118 42.096
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 2.79 2.96 96.2 0.39 3.43 3.6
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 2WHG 2.79 43.27 15312 806 100 0.20134 0.19861 0.1943 0.25318 0.2436 RANDOM 38.177
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] 0.57 0.13 -0.35 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.338 r_dihedral_angle_3_deg 20.277 r_dihedral_angle_4_deg 18.373 r_dihedral_angle_1_deg 7.412 r_sphericity_free 6.572 r_scangle_it 4.115 r_scbond_it 2.486 r_sphericity_bonded 2.361 r_mcangle_it 2.09 r_angle_refined_deg 1.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.338 r_dihedral_angle_3_deg 20.277 r_dihedral_angle_4_deg 18.373 r_dihedral_angle_1_deg 7.412 r_sphericity_free 6.572 r_scangle_it 4.115 r_scbond_it 2.486 r_sphericity_bonded 2.361 r_mcangle_it 2.09 r_angle_refined_deg 1.794 r_rigid_bond_restr 1.629 r_mcbond_it 1.162 r_angle_other_deg 0.984 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3454 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing