5HDD

Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 800 fs to 1200 fs Structure


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION295Combine and vortex 4.45M sodium malonate with 100 uL protein (135 mg/ml initial concentration) for a final sodium malonate concentration of 3.2M. Let stand at room temperature for 1 hour. Spin at 10,000g for 2 hours in small spin concentrators. Vortex and let stand at room temperature for 4 hours. Harvest crystals and rebuffer with 3.0M sodium malonate.
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-12015-03-21MSINGLE 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
11.619.3198.79104701304613046

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.619.311304665898.790.210240.20760.2648RANDOM5.206
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]
-0.02-0.01-0.020.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.721
r_dihedral_angle_3_deg18.773
r_dihedral_angle_4_deg15.579
r_dihedral_angle_1_deg8.478
r_angle_other_deg2.535
r_angle_refined_deg2.344
r_long_range_B_refined1.662
r_long_range_B_other1.386
r_mcangle_it0.53
r_mcangle_other0.529
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.721
r_dihedral_angle_3_deg18.773
r_dihedral_angle_4_deg15.579
r_dihedral_angle_1_deg8.478
r_angle_other_deg2.535
r_angle_refined_deg2.344
r_long_range_B_refined1.662
r_long_range_B_other1.386
r_mcangle_it0.53
r_mcangle_other0.529
r_scangle_other0.395
r_mcbond_it0.318
r_mcbond_other0.318
r_scbond_it0.244
r_scbond_other0.244
r_chiral_restr0.123
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
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