6NKN

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


X-RAY DIFFRACTION

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
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1GDVN
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1401209.5
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
198993108241

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2dyr2.510.52314481214398.540.177770.175650.21736RANDOM63.44
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
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
r_scbond_other5.517
r_mcbond_it4.834
r_mcbond_other4.829
r_angle_refined_deg1.696
r_angle_other_deg1.388
r_chiral_restr0.155
r_gen_planes_other0.017
r_gen_planes_refined0.01
r_bond_refined_d0.008
r_bond_other_d0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
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