5J7A

Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H68 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.6293Precipitant: 29%-38% PEG 2000, 100 mM phosphate buffer pH 5.6. MAG 9.9 used for LCP formation. Crystallization setup in Hamilton syringe with tube of LCP surrounded by precipitant.
Crystal Properties
Matthews coefficientSolvent content
2.550.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62α = 90
b = 62β = 90
c = 110γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELCS-PAD CXI-22014-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.83SLAC LCLSCXI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.321.999.986.561631102731.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4199.861.5816.8

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-VALUE1H682.321.661001065099.870.19260.1910.2181RANDOM39.282
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]
1.450.721.45-4.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.63
r_dihedral_angle_4_deg16.008
r_dihedral_angle_3_deg13.32
r_dihedral_angle_1_deg4.452
r_angle_refined_deg1.165
r_angle_other_deg0.89
r_mcangle_it0.694
r_mcbond_it0.37
r_mcbond_other0.37
r_chiral_restr0.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.63
r_dihedral_angle_4_deg16.008
r_dihedral_angle_3_deg13.32
r_dihedral_angle_1_deg4.452
r_angle_refined_deg1.165
r_angle_other_deg0.89
r_mcangle_it0.694
r_mcbond_it0.37
r_mcbond_other0.37
r_chiral_restr0.059
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1715
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing