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OhrB (Organic Hydroperoxide Resistance protein) wild type from Chromobacterium violaceum and reduced by DTT
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 291.15 Purified protein 10mg/ml in 5mM Tris-Hcl, pH 7.4 and DTT 10mM
Crystallization solution: Magnesium Chloride 200mM, BIS-TRIS 100mM pH 5.5, PEG 3,350 25%w/v
Then, Soaked with Cs + DTT 50mM
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.16 α = 90 b = 88.16 β = 90 c = 169.916 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 273.15 PIXEL DECTRIS PILATUS 2M 2016-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.458660 LNLS D03B-MX1
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 1.87 45.49 100 0.114 0.038 0.999 19 17.2 61621
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 1.87 1.91 100 2.798 1.275 0.356 9.3
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 6EB4 1.87 35 58510 3029 99.98 0.19415 0.19308 0.1994 0.21446 0.2162 RANDOM 40.783
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 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_4_deg 20.393 r_dihedral_angle_3_deg 14.948 r_dihedral_angle_1_deg 6.97 r_long_range_B_refined 6.484 r_long_range_B_other 6.47 r_scangle_other 3.425 r_mcangle_it 2.739 r_mcangle_other 2.739 r_scbond_other 2.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.18 r_dihedral_angle_4_deg 20.393 r_dihedral_angle_3_deg 14.948 r_dihedral_angle_1_deg 6.97 r_long_range_B_refined 6.484 r_long_range_B_other 6.47 r_scangle_other 3.425 r_mcangle_it 2.739 r_mcangle_other 2.739 r_scbond_other 2.183 r_scbond_it 2.182 r_angle_refined_deg 1.813 r_mcbond_it 1.705 r_mcbond_other 1.703 r_angle_other_deg 1.511 r_chiral_restr 0.08 r_bond_refined_d 0.015 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 4122 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing