5EBJ | pdb_00005ebj

Joint X-ray/neutron structure of reversibly photoswitching chromogenic protein, Dathail

NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	0.2M Magnesium Chloride, 0.1M Bis-Tris:HCl pH 6.5, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.209	α = 90
b = 82.049	β = 90
c = 40.889	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	293	ANGER CAMERA	ORNL	COLLIMATORS	2014-09-23	L	LAUE
2	1	x-ray	293	IMAGE PLATE	RIGAKU RAXIS IV++	OSMIC VARIMAX	2014-01-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ORNL Spallation Neutron Source BEAMLINE MANDI	2.0-4.0	ORNL Spallation Neutron Source	MANDI
2	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	2.5	40	63.6	0.317						3.9	1.4		6158	2.5
2	2.1	40	96.6	0.05						25.3	3.8		15273	2.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.56		0.263						2.2	0.8
2	2.1	2.18		0.584						2.2	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.5	40		2.5	9281	5652	274	60			0.305		0.344		RANDOM	43.44
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.1	40		2.5	15778	11878	489	75.2			0.235	0.23	0.253	0.25	RANDOM	43.44

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
Key	Refinement Restraint Deviation
x_torsion_deg	17.3
x_angle_deg	1.3
x_torsion_impr_deg	0.97
x_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1746
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms

Software

Software
Software Name	Purpose
nCNS	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Mantid	data reduction
SHELXPREP	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.