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azide-bound cytochrome c oxidase structure determined using the crystals exposed to 2 mM azide solution for 2 days
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 PEG 4000, Sodium phosphate
Crystal Properties Matthews coefficient Solvent content 4.1 70.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.379 α = 90 b = 206.655 β = 90 c = 177.589 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 50 CCD RAYONIX MX225HE 2014-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.9 200 99.9 0.112 0.116 0.031 12.2 12.6 523084
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 1.92 100 0.848 0.892 0.274 0.933 10.2
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 5B1A 1.9 40 496443 26411 99.65 0.1653 0.164 0.1652 0.1892 0.1898 RANDOM 42.928
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] 2.04 1.84 -3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35 r_dihedral_angle_4_deg 16.088 r_dihedral_angle_3_deg 15.182 r_dihedral_angle_1_deg 6.589 r_angle_refined_deg 2.583 r_chiral_restr 0.212 r_bond_refined_d 0.029 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28506 Nucleic Acid Atoms Solvent Atoms 1674 Heterogen Atoms 2676
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing