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OhrA (Organic Hydroperoxide Resistance protein) wild type from chromobacterium violaceum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N2F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291.15 Purified OhrA protein 10mg/ml in 5mM Tris-Hcl pH 7.4
Crystallisation conditions: Potassium Sodium Tartrate 200mM, Tri-Sodium Citrate 100mM pH 5.5, Ammonium Sulfate 2M
Crystal Properties Matthews coefficient Solvent content 3.74 67.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.094 α = 90 b = 138.094 β = 90 c = 45.116 γ = 120
Symmetry Space Group P 32 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 80 PIXEL DECTRIS PILATUS 6M 2016-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 36.01 97.4 0.052 0.054 0.017 1 26.9 19.7 94442
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 3.912 1.241 0.516 0.8 19.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1N2F 1.4 36 89670 4705 97.35 0.15272 0.15132 0.17916 0.1865 RANDOM 32.371
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] 0.48 0.24 0.48 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.904 r_dihedral_angle_4_deg 16.736 r_rigid_bond_restr 14.251 r_dihedral_angle_3_deg 13.343 r_mcbond_it 9.126 r_mcbond_other 9.099 r_long_range_B_refined 8.117 r_long_range_B_other 8.023 r_scangle_other 7.311 r_mcangle_other 7.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.904 r_dihedral_angle_4_deg 16.736 r_rigid_bond_restr 14.251 r_dihedral_angle_3_deg 13.343 r_mcbond_it 9.126 r_mcbond_other 9.099 r_long_range_B_refined 8.117 r_long_range_B_other 8.023 r_scangle_other 7.311 r_mcangle_other 7.06 r_mcangle_it 7.051 r_scbond_it 6.829 r_scbond_other 6.826 r_dihedral_angle_1_deg 5.982 r_angle_refined_deg 1.667 r_angle_other_deg 1.508 r_chiral_restr 0.082 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2131 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing