3SS2 | pdb_00003ss2

Neutron structure of perdeuterated rubredoxin using 48 hours 3rd pass data

NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KYW	PDB ENTRY 3KYW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20 mg/ml rubredoxin in 1.9m sodium/potassium phosphate sitting drop equilibrated against 3.8 m sodium/potassium phosphate reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.92	α = 90
b = 34.928	β = 90
c = 43.532	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	293	IMAGE PLATE	MAATEL QLD: LADI-III		2008-05-07	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ILL BEAMLINE LADI III	3.2 - 4.2	ILL	LADI III

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	1.65	26.76	70.2	9.5	4.1	6589	4550		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.74	24.7		0.171	3.9	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
NEUTRON DIFFRACTION	FOURIER SYNTHESIS	PDB ENTRY 3KYW	1.75	24.334	1.53	4283	205	77.19	0.212	0.2105	0.2424

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]
-2.6843			1.3125		1.8941

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.778
f_angle_d	1.183
f_chiral_restr	0.065
f_bond_d	0.011
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	394
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	1

Software

Software
Software Name	Purpose
LAUEGEN	data collection
PHENIX	refinement
LAUEGEN	data reduction
SCALA	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.