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Crystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2M Potassium bromide,
0.1M Tris pH 7.5,
10% PEG1000,
10% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.431 α = 90 b = 38.612 β = 97.63 c = 59.644 γ = 90
Symmetry Space Group P 1 21 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 2014-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.3 99.2 0.048 0.053 20.13 35883 -3 16.269
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.33 99.5 0.247 0.272 5.25
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 4TXV 1.3 59.12 34089 1795 99.2 0.1102 0.1089 0.1336 0.151 RANDOM 16.637
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] -0.28 -0.08 0.46 -0.16
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.673 r_dihedral_angle_2_deg 35.294 r_sphericity_bonded 15.054 r_dihedral_angle_4_deg 14.59 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 8.812 r_rigid_bond_restr 6.327 r_mcangle_it 3.219 r_mcbond_it 2.457 r_mcbond_other 2.409
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.673 r_dihedral_angle_2_deg 35.294 r_sphericity_bonded 15.054 r_dihedral_angle_4_deg 14.59 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 8.812 r_rigid_bond_restr 6.327 r_mcangle_it 3.219 r_mcbond_it 2.457 r_mcbond_other 2.409 r_angle_refined_deg 2.27 r_angle_other_deg 1.238 r_chiral_restr 0.131 r_bond_refined_d 0.026 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1091 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing XSCALE data reduction