7THU

Structure of reduced bovine cytochrome c oxidase at 1.93 Angstrom resolution obtained by synchrotron X-rays


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DYR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.8277PEG 4000, Postassium phosphate, Decylmaltoside
Crystal Properties
Matthews coefficientSolvent content
4.1370.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.182α = 90
b = 182.282β = 90
c = 208.683γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9340.00399.20.99912.66.8500705
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.932.030.4161

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2DYR1.9340.0035005542468199.1290.1850.18360.212546.817
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]
-2.323-0.7273.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.506
r_dihedral_angle_4_deg16.537
r_dihedral_angle_other_3_deg16.375
r_dihedral_angle_3_deg16.33
r_lrange_other9.075
r_lrange_it9.072
r_scangle_it7.166
r_scangle_other7.165
r_dihedral_angle_1_deg6.422
r_mcangle_it4.968
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.506
r_dihedral_angle_4_deg16.537
r_dihedral_angle_other_3_deg16.375
r_dihedral_angle_3_deg16.33
r_lrange_other9.075
r_lrange_it9.072
r_scangle_it7.166
r_scangle_other7.165
r_dihedral_angle_1_deg6.422
r_mcangle_it4.968
r_mcangle_other4.968
r_scbond_it4.965
r_scbond_other4.965
r_mcbond_it3.641
r_mcbond_other3.641
r_chiral_restr_other2.042
r_angle_refined_deg1.809
r_angle_other_deg1.424
r_nbd_other0.225
r_nbd_refined0.214
r_symmetry_nbd_other0.187
r_nbtor_refined0.178
r_symmetry_xyhbond_nbd_other0.177
r_symmetry_nbd_refined0.166
r_symmetry_xyhbond_nbd_refined0.158
r_xyhbond_nbd_refined0.152
r_chiral_restr0.143
r_symmetry_nbtor_other0.092
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28584
Nucleic Acid Atoms
Solvent Atoms1381
Heterogen Atoms2730

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing