6ZH7

Crystal structure of fatty acid photodecarboxylase in the dark state determined by serial femtosecond crystallography at room temperature


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YRU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE5.5281.1519% (w/v) PEG 4000, 0.1 M sodium citrate pH 5.5, 10 mM spermidine
Crystal Properties
Matthews coefficientSolvent content
2.7655.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.39α = 90
b = 60.01β = 90.6
c = 182.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277.15PIXELCS-PAD CXI-12018-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.3SLAC LCLSCXI

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
12251000.9820.1515.635593061
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051000.5480.685236

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 REPLACEMENTFREE R-VALUE6YRU224.9585938436499.890.1980.19630.2312RANDOM29.803
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]
1.13-1.56-1.190.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.365
r_dihedral_angle_4_deg17.978
r_dihedral_angle_3_deg15.944
r_dihedral_angle_1_deg7.206
r_angle_refined_deg1.491
r_angle_other_deg1.286
r_chiral_restr0.066
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.365
r_dihedral_angle_4_deg17.978
r_dihedral_angle_3_deg15.944
r_dihedral_angle_1_deg7.206
r_angle_refined_deg1.491
r_angle_other_deg1.286
r_chiral_restr0.066
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8417
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms166

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
Cootmodel building