7E71

Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 ms structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UG9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE6.9293100 mM MES, pH 6.9, 100 mM Na formate, and 30% PEG500DM
Crystal Properties
Matthews coefficientSolvent content
2.6253.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.8α = 90
b = 142.2β = 90
c = 94.7γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMPCCD2016-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL31.77SACLABL3

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
12.439.411000.99090.0897.08168.916730
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)
12.42.4411000.55851.1106155.2

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 REPLACEMENTTHROUGHOUT3ug92.514.961062155475.440.41320.41060.4634RANDOM67.203
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]
1.29-4.73.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.574
r_dihedral_angle_3_deg19.762
r_dihedral_angle_4_deg19.607
r_dihedral_angle_1_deg5.825
r_angle_refined_deg1.541
r_angle_other_deg1.214
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.574
r_dihedral_angle_3_deg19.762
r_dihedral_angle_4_deg19.607
r_dihedral_angle_1_deg5.825
r_angle_refined_deg1.541
r_angle_other_deg1.214
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2317
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms174

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing