6NKN | pdb_00006nkn

Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room temperature


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.827736 hour crystallization in a cold room with stirring
Crystal Properties
Matthews coefficientSolvent content
4.472.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.7α = 90
b = 189.8β = 90
c = 211.3γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELCS-PAD XPP2016-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.306SLAC LCLSMFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
140 (fs)1209.5 (KeV)
Data Reduction
Diffraction IDFrames IndexedCrystal HitsFrames IndexedLatices Merged
19899310824198993
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1GDVNundefined (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
12.510.598.540.9895.11038231448
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)
12.52.5611000.1680.56

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2dyr2.510.52314481214398.540.177770.175650.180.217360.22RANDOM63.44
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]
-2.50.951.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.896
r_dihedral_angle_3_deg17.771
r_dihedral_angle_4_deg17.572
r_long_range_B_refined11.656
r_long_range_B_other11.656
r_scangle_other8.667
r_mcangle_it7.367
r_mcangle_other7.367
r_dihedral_angle_1_deg7.099
r_scbond_it5.517
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28419
Nucleic Acid Atoms
Solvent Atoms772
Heterogen Atoms2228

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing