5HD5 | pdb_00005hd5

Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 200 ns time delay photo-activated (light) structure


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION7295Microcrystalization using combination free interface diffusion and spin centrifugation.
Crystal Properties
Matthews coefficientSolvent content
1.8834.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.9α = 90
b = 66.9β = 90
c = 40.8γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295PIXELCS-PAD CXI-12015-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.31SLAC LCLSCXI

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
11.619.2998.931022871306613066

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.619.291306665898.930.293220.289430.280.373880.36RANDOM8.571
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]
-0.12-0.06-0.120.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.9
r_dihedral_angle_3_deg17.053
r_dihedral_angle_1_deg6.733
r_dihedral_angle_4_deg6.439
r_long_range_B_refined5.95
r_long_range_B_other5.799
r_scangle_other2.168
r_angle_refined_deg2.069
r_mcangle_it1.658
r_mcangle_other1.657
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms987
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling