5B35

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B34PDB ID: 5B34

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE29325%(w/v) DMPC/CHAPSO bicelles, 3.2 M NaH2PO4, 3.5%(w/v) triethylene glycol, 180 mM 1,6-hexanediol
Crystal Properties
Matthews coefficientSolvent content
2.8456.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.2α = 90
b = 103β = 90
c = 128.7γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMPCCD2014-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL31.771SACLABL3

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
12.35501004.8380.913212
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.42

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 REPLACEMENTTHROUGHOUTPDB ID: 5B342.35501253565099.970.169050.166330.21978RANDOM66.323
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]
0.180.14-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.806
r_dihedral_angle_3_deg17.703
r_dihedral_angle_4_deg16.393
r_long_range_B_refined9.102
r_long_range_B_other9.097
r_scangle_other7.643
r_dihedral_angle_1_deg5.401
r_scbond_it5.342
r_scbond_other5.34
r_mcangle_other5.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.806
r_dihedral_angle_3_deg17.703
r_dihedral_angle_4_deg16.393
r_long_range_B_refined9.102
r_long_range_B_other9.097
r_scangle_other7.643
r_dihedral_angle_1_deg5.401
r_scbond_it5.342
r_scbond_other5.34
r_mcangle_other5.046
r_mcangle_it5.044
r_mcbond_it3.832
r_mcbond_other3.82
r_angle_refined_deg1.945
r_angle_other_deg1.087
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1745
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms205

Software

Software
Software NamePurpose
REFMACrefinement
Cheetahdata extraction
CrystFELdata processing
SHELXphasing