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High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AR1 PDB entry 1AR1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 277 25% glycerol, pH 5.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.02 69.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.403 α = 90 b = 150.473 β = 90 c = 157.185 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 CCD MARMOSAIC 225 mm CCD 2005-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9198 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 111.8 99.04 0.124 14.2 4.9 90709 90709 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.32 98.3 0.379 3.2 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1AR1 2.25 19.98 -3 90709 90709 2819 99.04 0.22024 0.22024 0.21836 0.2108 0.27996 0.2701 RANDOM 45.272
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.795 r_scangle_it 5.166 r_scbond_it 3.538 r_angle_refined_deg 2.683 r_mcangle_it 2.407 r_mcbond_it 1.381 r_symmetry_vdw_refined 0.323 r_symmetry_hbond_refined 0.313 r_nbd_refined 0.264 r_xyhbond_nbd_refined 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.795 r_scangle_it 5.166 r_scbond_it 3.538 r_angle_refined_deg 2.683 r_mcangle_it 2.407 r_mcbond_it 1.381 r_symmetry_vdw_refined 0.323 r_symmetry_hbond_refined 0.313 r_nbd_refined 0.264 r_xyhbond_nbd_refined 0.234 r_chiral_restr 0.23 r_bond_refined_d 0.031 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7956 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 883
Software Software Software Name Purpose MAR345dtb data collection EPMR phasing REFMAC refinement XDS data reduction XSCALE data scaling