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The structure of azide-bound cytochrome c oxidase determined using the another batch crystals exposed to 20 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 PEG4000, Sodium phosphate
Crystal Properties Matthews coefficient Solvent content 4.08 69.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.126 α = 90 b = 205.893 β = 90 c = 177.576 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 1.85 200 99.9 0.122 0.127 0.032 11.4 15.8 561432
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 1.85 1.87 100 1.108 1.147 0.294 0.921 14.9
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 1.85 40 532947 28239 99.3 0.1645 0.1632 0.165 0.1887 0.1906 RANDOM 40.336
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] 0.23 3.22 -3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.298 r_dihedral_angle_4_deg 16.254 r_dihedral_angle_3_deg 15.312 r_dihedral_angle_1_deg 6.606 r_angle_refined_deg 2.645 r_chiral_restr 0.218 r_bond_refined_d 0.03 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28506 Nucleic Acid Atoms Solvent Atoms 1618 Heterogen Atoms 2708
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing