8GCQ | pdb_00008gcq

SFX structure of oxidized cytochrome c oxidase at 2.38 Angstrom resolution


X-RAY DIFFRACTION

Serial Crystallography (SX)

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
1MESHundefined (µl/min)undefined (µm)

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.38332850361418299.9220.2340.23220.230.26570.2732.959
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
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