5MG1

Structure of the photosensory module of Deinococcus phytochrome by serial femtosecond X-ray crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O9CPAS-GAF from PDB 2O9C, and PHY domain from 4Q0J
experimental modelPDB 4Q0JPAS-GAF from PDB 2O9C, and PHY domain from 4Q0J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.5298PEG 3350, Tacsimate pH 6.0, Tacsimate pH 7.0, ethylene glycol, PIPES-NaOH pH 6.5
Crystal Properties
Matthews coefficientSolvent content
4.4372.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.7α = 90
b = 151.7β = 90
c = 151.2γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX170-HSCompound refractive lenses2015-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE MFX1.305SLAC LCLSMFX

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
13.3131.37699.860.86329.23439.1615996
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)
13.33.356999.870.1784.06920.75

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPAS-GAF from PDB 2O9C, and PHY domain from 4Q0J3.337.8941.341596882099.940.21350.21170.244791.6934
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_d17.379
f_angle_d0.562
f_chiral_restr0.038
f_plane_restr0.004
f_bond_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3726
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms43

Software

Software
Software NamePurpose
cctbx.xfeldata collection
cctbx.primedata reduction
cctbx.xfeldata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
psanadata reduction