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A H224Y mutant for VIM-7 from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y8B PDB ENTRY 2Y8B
Crystallization Crystal Properties Matthews coefficient Solvent content 2.05 40.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.225 α = 90 b = 70.225 β = 90 c = 47.027 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 MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
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 1.4 30 96.6 0.07 9.1 3.5 43649 12.8
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 1.4 1.48 86.8 0.16 2
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 2Y8B 1.4 25 41427 2196 96.44 0.11969 0.11776 0.1311 0.15636 0.1641 RANDOM 14.582
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] -0.08 -0.08 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.635 r_sphericity_free 29.736 r_dihedral_angle_4_deg 19.094 r_dihedral_angle_3_deg 11.44 r_sphericity_bonded 11.366 r_dihedral_angle_1_deg 6.644 r_rigid_bond_restr 5.495 r_angle_refined_deg 1.52 r_angle_other_deg 1.101 r_chiral_restr 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.635 r_sphericity_free 29.736 r_dihedral_angle_4_deg 19.094 r_dihedral_angle_3_deg 11.44 r_sphericity_bonded 11.366 r_dihedral_angle_1_deg 6.644 r_rigid_bond_restr 5.495 r_angle_refined_deg 1.52 r_angle_other_deg 1.101 r_chiral_restr 0.322 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 1710 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing