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Structure of a putative epoxide hydrolase from Pseudomonas aeruginosa, with bound MFA.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y37 PDB ENTRY 1Y37
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1 M LI2SO4, 1.25 M (NH4)2SO4, 0.1 M TRIS HCL PH 8.5
Crystal Properties Matthews coefficient Solvent content 3.67 66.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.92 α = 90 b = 83.92 β = 90 c = 140.95 γ = 90
Symmetry Space Group P 41 21 2
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 QUANTUM 315r 2012-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 36.83 99.7 0.09 11.5 6.2 99408 2 13.7
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 99.3 0.69 2.4 5
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 1Y37 1.4 36.27 94130 4952 99.68 0.11165 0.1104 0.1309 0.13525 0.1521 RANDOM 17.522
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.614 r_dihedral_angle_2_deg 30.306 r_dihedral_angle_4_deg 19.155 r_sphericity_bonded 12.522 r_dihedral_angle_3_deg 12.136 r_mcbond_other 11.304 r_mcbond_it 10.937 r_dihedral_angle_1_deg 5.334 r_rigid_bond_restr 3.69 r_angle_refined_deg 1.72
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.614 r_dihedral_angle_2_deg 30.306 r_dihedral_angle_4_deg 19.155 r_sphericity_bonded 12.522 r_dihedral_angle_3_deg 12.136 r_mcbond_other 11.304 r_mcbond_it 10.937 r_dihedral_angle_1_deg 5.334 r_rigid_bond_restr 3.69 r_angle_refined_deg 1.72 r_angle_other_deg 0.912 r_symmetry_vdw_refined 0.311 r_nbd_refined 0.279 r_nbd_other 0.221 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.188 r_symmetry_vdw_other 0.179 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.113 r_nbtor_other 0.107 r_xyhbond_nbd_other 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 2346 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing