5HDC

Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 100 fs to 400 fs Structure

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	7	295	Combine 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 coefficient	Solvent content
1.88	34.5

Crystal Data

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

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	PIXEL	CS-PAD CXI-1		2015-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.31	SLAC LCLS	CXI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	19.31	98.72	10	300	13039	13039

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.6	19.31	13039	655	98.72	0.21068	0.2083	0.25832	RANDOM	5.462

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]
-0.01	-0.01		-0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.61
r_dihedral_angle_4_deg	24.443
r_dihedral_angle_3_deg	21.6
r_dihedral_angle_1_deg	8.04
r_long_range_B_refined	2.993
r_long_range_B_other	2.651
r_angle_other_deg	2.557
r_angle_refined_deg	2.372
r_mcangle_it	0.713
r_mcangle_other	0.712
r_scangle_other	0.509
r_mcbond_it	0.413
r_mcbond_other	0.413
r_scbond_it	0.313
r_scbond_other	0.313
r_chiral_restr	0.132
r_bond_refined_d	0.022
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	987
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling