9V6B | pdb_00009v6b

Neutron crystal structure of the oxidized form of b5R at pD 6.5

NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GV8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	12% PEG 3350, 10mM potassium phosphate pD 6.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.628	α = 90
b = 72.233	β = 90
c = 85.08	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	100	DIFFRACTOMETER	iBIX		2014-05-24	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	2.6-4.4	JPARC MLF	BL-03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	20	96.2	0.194	0.104	0.98	6.6	4.1		38402			9.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	93.1		0.509	0.318	0.758	2.2	3.1

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	16.44	38394	1971	95.39	0.1801	0.1789	0.2015	Select the same reflections as PDB code 5GV8	13.63

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
f_dihedral_angle_d	17.442
f_angle_d	1.52
f_chiral_restr	0.083
f_bond_d	0.02
f_plane_restr	0.011

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.