8Z6K | pdb_00008z6k

SFX structure of CraCRY 166 ms after photoexcitation of the oxidized protein


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FN3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE5.62770.1 M MES, pH 5.6 (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.244.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.74α = 90
b = 65.45β = 90
c = 152.95γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMPCCD2021-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL21.24SACLABL2

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
110 (fs)301.7710 (KeV)
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
1High viscosity injector0.76 (µl/min)undefined (µm)50grease

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
11.833.0299.790.9998.6912314817124.01
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)
11.81.841000.4421.09132

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6FN32.230.092660583299.860.20810.20770.20770.21980.219824.75
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.6524
f_angle_d1.0435
f_chiral_restr0.0573
f_plane_restr0.0087
f_bond_d0.0069
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3897
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms54

Software

Software
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
pointlessdata scaling
REFMACphasing