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OhrB (Organic Hydroperoxide Resistance protein) mutant (C60A) from Chromobacterium violaceum, interacting with dihydrolipoamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291.15 Purified Ohr_C60A protein 10mg/ml in 5mM Tris-Hcl pH 7.4
Crystallisation conditions: Magnesium Clhoride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v
crystal was soaked for 10min in Lipoamide 5mM, solved in 5% ethanol and Crystallisation condition
Crystal Properties Matthews coefficient Solvent content 2.96 62.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.675 α = 90 b = 87.675 β = 90 c = 179.609 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 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) 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 2.61 43.84 99.9 0.343 0.105 1 10.82 20.8 23763
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.61 2.73 1.526 0.41
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 6EB4 2.61 35 22467 1238 99.85 0.19633 0.19424 0.199 0.23214 0.2344 RANDOM 71.207
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] 0.6 0.3 0.6 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.303 r_dihedral_angle_4_deg 23.98 r_dihedral_angle_3_deg 18.006 r_long_range_B_refined 7.814 r_long_range_B_other 7.813 r_dihedral_angle_1_deg 7.625 r_scangle_other 5.383 r_mcangle_it 4.868 r_mcangle_other 4.867 r_scbond_it 3.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.303 r_dihedral_angle_4_deg 23.98 r_dihedral_angle_3_deg 18.006 r_long_range_B_refined 7.814 r_long_range_B_other 7.813 r_dihedral_angle_1_deg 7.625 r_scangle_other 5.383 r_mcangle_it 4.868 r_mcangle_other 4.867 r_scbond_it 3.329 r_scbond_other 3.328 r_mcbond_it 2.994 r_mcbond_other 2.994 r_angle_refined_deg 1.83 r_angle_other_deg 1.371 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 4100 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing