6NMP

SFX structure of oxidized cytochrome c oxidase at room temperature


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.827736 hour crystallization in a cold room with stirring
Crystal Properties
Matthews coefficientSolvent content
4.3671.82

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
1GCVN
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1401209.5

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
12.91599.640.9282.8204150666
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)
12.92.9720.1490.43

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 REPLACEMENTTHROUGHOUT2DYR2.915149982780599.190.194280.19170.24357RANDOM63.835
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]
-2.460.721.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.813
r_dihedral_angle_3_deg17.699
r_dihedral_angle_4_deg17.396
r_long_range_B_refined10.217
r_long_range_B_other10.212
r_dihedral_angle_1_deg6.544
r_scangle_other6.537
r_mcangle_it5.887
r_mcangle_other5.887
r_scbond_it3.933
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.813
r_dihedral_angle_3_deg17.699
r_dihedral_angle_4_deg17.396
r_long_range_B_refined10.217
r_long_range_B_other10.212
r_dihedral_angle_1_deg6.544
r_scangle_other6.537
r_mcangle_it5.887
r_mcangle_other5.887
r_scbond_it3.933
r_scbond_other3.933
r_mcbond_it3.568
r_mcbond_other3.568
r_angle_refined_deg1.666
r_angle_other_deg1.115
r_chiral_restr0.104
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.004
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 Atoms28506
Nucleic Acid Atoms
Solvent Atoms476
Heterogen Atoms2228

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing