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Low-dose structure of bovine heart cytochrome c oxidase in the fully oxidized state determined using 30 keV X-ray
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.8 277 PEG 4000
Crystal Properties Matthews coefficient Solvent content 4.01 69.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.02 α = 90 b = 203.54 β = 90 c = 177.41 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 X CdTe 300K Undulator 3rd harmonic, Compound refractive lends 2016-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.4133 SPring-8 BL41XU
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 1.9 40 98.09 0.099 0.11 0.047 0.994 8.1 4.9 503312 38.511
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 96.33 0.973 1.116 0.535 0.697 1.4 4.23
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 5B1B 1.9 40 478268 25030 98.03 0.1735 0.1721 0.1747 0.1992 0.2251 RANDOM 42.87
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] 0.42 0.86 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.226 r_dihedral_angle_4_deg 17.139 r_dihedral_angle_3_deg 15.01 r_dihedral_angle_1_deg 5.921 r_sphericity_bonded 5.461 r_rigid_bond_restr 4.571 r_angle_refined_deg 1.659 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28506 Nucleic Acid Atoms Solvent Atoms 2558 Heterogen Atoms 2234
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing