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Azide-bound cytochrome c oxidase structure determined using the crystals exposed to 10 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 4.04 69.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.33 α = 90 b = 204.832 β = 90 c = 177.691 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 1.65 200 99.9 0.09 0.094 0.029 13 10 791265
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 1.65 1.66 100 0.883 0.937 0.31 0.895 9
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 1.65 40 748257 39618 99.85 0.1629 0.1619 0.1642 0.182 0.1835 RANDOM 37.48
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] -0.58 3.08 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.099 r_dihedral_angle_3_deg 15.184 r_dihedral_angle_4_deg 15.068 r_dihedral_angle_1_deg 6.479 r_angle_refined_deg 2.911 r_chiral_restr 0.239 r_bond_refined_d 0.032 r_gen_planes_refined 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28506 Nucleic Acid Atoms Solvent Atoms 1679 Heterogen Atoms 2733
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing