☰ Navigation Tabs
A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate
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, HANGING DROP 7.3 291 MPEG 2000 is contained in the crystallization buffer pH 5.5, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.1 70.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.461 α = 90 b = 151.332 β = 90 c = 157.487 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 2006-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.92021 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 2.32 20 98.8 0.09 19.14 87146 87146 -3 -3 51.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.32 2.4 97 3.93 8161
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 2.32 19.69 -3 86853 84230 2623 100 0.20618 0.20618 0.20505 0.2037 0.2424 0.2049 RANDOM 60.153
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_2_deg 37.705 r_dihedral_angle_4_deg 25.498 r_dihedral_angle_3_deg 19.058 r_dihedral_angle_1_deg 7.709 r_mcangle_it 5.882 r_scangle_it 5.773 r_mcbond_it 4.385 r_scbond_it 4.243 r_angle_refined_deg 2.488 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.705 r_dihedral_angle_4_deg 25.498 r_dihedral_angle_3_deg 19.058 r_dihedral_angle_1_deg 7.709 r_mcangle_it 5.882 r_scangle_it 5.773 r_mcbond_it 4.385 r_scbond_it 4.243 r_angle_refined_deg 2.488 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.251 r_xyhbond_nbd_refined 0.197 r_metal_ion_refined 0.184 r_chiral_restr 0.182 r_symmetry_hbond_refined 0.05 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7954 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 703
Software Software Software Name Purpose SBC-Collect data collection DM model building REFMAC refinement XDS data reduction XSCALE data scaling DM phasing