8GCQ

SFX structure of oxidized cytochrome c oxidase at 2.38 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7TIE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.8277PEG4000, Sodium Phosphate, decylmaltoside
Crystal Properties
Matthews coefficientSolvent content
4.3571.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.6α = 90
b = 189.5β = 90
c = 211.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDRAYONIX MX340-HS2022-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.24SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1MESH

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
12.38331000.97464.68864.9426285036
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)
12.382.470.0472

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.38332850361418299.9220.2340.23220.265732.959
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]
-0.0370.054-0.018
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.975
r_dihedral_angle_3_deg18.865
r_dihedral_angle_4_deg18.432
r_lrange_it9.742
r_lrange_other9.691
r_dihedral_angle_1_deg7.875
r_dihedral_angle_other_3_deg6.401
r_mcangle_it5.051
r_mcangle_other5.051
r_scangle_it4.825
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.975
r_dihedral_angle_3_deg18.865
r_dihedral_angle_4_deg18.432
r_lrange_it9.742
r_lrange_other9.691
r_dihedral_angle_1_deg7.875
r_dihedral_angle_other_3_deg6.401
r_mcangle_it5.051
r_mcangle_other5.051
r_scangle_it4.825
r_scangle_other4.825
r_mcbond_it3.167
r_mcbond_other3.167
r_scbond_it2.958
r_scbond_other2.958
r_angle_refined_deg1.742
r_angle_other_deg1.145
r_metal_ion_refined0.385
r_symmetry_xyhbond_nbd_refined0.271
r_xyhbond_nbd_refined0.236
r_nbd_refined0.234
r_symmetry_nbd_other0.201
r_nbd_other0.2
r_symmetry_nbd_refined0.181
r_nbtor_refined0.179
r_symmetry_xyhbond_nbd_other0.107
r_symmetry_nbtor_other0.083
r_chiral_restr0.07
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28496
Nucleic Acid Atoms
Solvent Atoms601
Heterogen Atoms2368

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing