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OhrA (Organic Hydroperoxide Resistance protein) mutant (C61S) in the "open conformation" from chromobacterium violaceum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ECY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 purified ohr protein at 10mg/ml in 5mM Tris-Hcl, pH 7.4 & 50mM NaCl)
Crystallisation conditions: Ammonium sulfate 200mM, Sodium acetate 100mM pH 4, PEG 2,000 30%w/v
Crystal Properties Matthews coefficient Solvent content 1.89 34.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.963 α = 90 b = 41.963 β = 90 c = 123.586 γ = 120
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 2017-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.44 36.34 97.9 0.038 0.017 1 25.5 10.1 43151
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 1.44 1.47 84.1 2.629 1.261 0.547 8.3
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 6ECY 1.44 35 41062 2048 97.87 0.19239 0.19135 0.2001 0.21321 0.2173 RANDOM 34.914
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] 1.39 0.69 1.39 -4.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.391 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_4_deg 10.914 r_dihedral_angle_1_deg 6.28 r_long_range_B_refined 4.445 r_long_range_B_other 4.422 r_scangle_other 2.546 r_scbond_it 1.75 r_mcangle_other 1.71 r_mcangle_it 1.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.391 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_4_deg 10.914 r_dihedral_angle_1_deg 6.28 r_long_range_B_refined 4.445 r_long_range_B_other 4.422 r_scangle_other 2.546 r_scbond_it 1.75 r_mcangle_other 1.71 r_mcangle_it 1.709 r_scbond_other 1.669 r_angle_refined_deg 1.621 r_angle_other_deg 1.496 r_mcbond_it 1.158 r_mcbond_other 1.153 r_chiral_restr 0.541 r_bond_refined_d 0.012 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2083 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing