7VSO

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with HAD16 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 5B35 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE29325%(W/V) DMPC/CHAPSO BICELLES, 3.2 M REMARK 280 NAH2PO4, 3.5%(W/V) TRIETHYLENE GLYCOL, 180 MM 1,6-HEXANEDIOL, 4 MM HAD16
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-ray293CCDMPCCD2015-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL31.771SACLABL3

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
12.3542.91000.9917.34206.213211
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)
12.352.430.488

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 REPLACEMENTTHROUGHOUT5B352.3542.91253065099.920.160250.157610.20982RANDOM79.264
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]
1.64-1.21-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.44
r_dihedral_angle_3_deg17.501
r_dihedral_angle_4_deg16.637
r_long_range_B_refined10.682
r_scbond_it8.309
r_mcangle_it5.992
r_mcbond_it5.169
r_dihedral_angle_1_deg4.645
r_angle_refined_deg1.955
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.44
r_dihedral_angle_3_deg17.501
r_dihedral_angle_4_deg16.637
r_long_range_B_refined10.682
r_scbond_it8.309
r_mcangle_it5.992
r_mcbond_it5.169
r_dihedral_angle_1_deg4.645
r_angle_refined_deg1.955
r_chiral_restr0.116
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1741
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms253

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
Cootmodel building