8GBT

Time-resolve SFX structure of a photoproduct of carbon monoxide complex of bovine cytochrome c oxidase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.8277PEG4000, Sodium Phosphate, decylmaltoside

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.3α = 90
b = 189β = 90
c = 209γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELCS-PAD CXI-12016-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.321SLAC LCLSCXI

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection

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
11.75932.451000.8596.926.9172414
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)
12.872.991000.226

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 REPLACEMENTTHROUGHOUT2.832.002172414868899.3550.2250.2230.268758.179
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]
-1.650.9490.701
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.052
r_dihedral_angle_3_deg18.243
r_dihedral_angle_other_3_deg16.272
r_dihedral_angle_4_deg15.967
r_lrange_it9.789
r_lrange_other9.789
r_dihedral_angle_1_deg7.345
r_scangle_it6.493
r_scangle_other6.493
r_mcangle_it6.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.052
r_dihedral_angle_3_deg18.243
r_dihedral_angle_other_3_deg16.272
r_dihedral_angle_4_deg15.967
r_lrange_it9.789
r_lrange_other9.789
r_dihedral_angle_1_deg7.345
r_scangle_it6.493
r_scangle_other6.493
r_mcangle_it6.053
r_mcangle_other6.053
r_scbond_it3.927
r_scbond_other3.927
r_mcbond_it3.717
r_mcbond_other3.716
r_angle_refined_deg1.553
r_angle_other_deg1.13
r_nbd_refined0.217
r_symmetry_nbd_refined0.215
r_symmetry_nbd_other0.18
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.163
r_nbd_other0.16
r_symmetry_xyhbond_nbd_refined0.13
r_symmetry_xyhbond_nbd_other0.101
r_symmetry_nbtor_other0.083
r_chiral_restr0.072
r_metal_ion_refined0.059
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28488
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms2248

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing