6NAC

Crystal structure of [FeFe]-hydrogenase I (CpI) solved with single pulse free electron laser data


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C8Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.629825% PEG 4000, 0.1M Sodium acetate (pH 4.6), 0.1M Sodium sulfate,
Crystal Properties
Matthews coefficientSolvent content
2.4549.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.165α = 90
b = 111.165β = 90
c = 104.007γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELCS-PAD CXI-12017-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE XPP1.3099SLAC LCLSXPP

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5533.195.50.65215.56.6903988.44
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6183.30.8381.74

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3C8Y1.5533.0971.3490327201495.50.24050.23950.2849
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.372
f_angle_d0.627
f_chiral_restr0.051
f_plane_restr0.004
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4451
Nucleic Acid Atoms
Solvent Atoms657
Heterogen Atoms65

Software

Software
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction
cctbx.primedata scaling
MOLREPphasing