3KYX | pdb_00003kyx

Joint Xray/neutron crystal structure determination of fully perdeuterated rubredoxin at 295K

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BRF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop			3.8 M sodium/potassium phosphate, hanging drop

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.374	α = 90
b = 35.339	β = 90
c = 44.111	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	x-ray	295	IMAGE PLATE	MAR345			M	SINGLE WAVELENGTH
2	1	neutron	295	IMAGE PLATE	MAATEL LADI-III		2008-05-07	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		1.54
2	NUCLEAR REACTOR		3.3-4.2

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	1.675	27.116	82.3	0.095	0.095					14.9	6.1		6814

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	1.675	1.77		0.099	0.099					7	1.4	304
1	1.77	1.87		0.101	0.101					6.7	2.9	622
1	1.87	2		0.098	0.098					6.8	5.7	706
1	2	2.16		0.1	0.1					6.4	7.7	701
1	2.16	2.37		0.102	0.102					5.8	7.9	673
1	2.37	2.65		0.099	0.099					6.1	7	629
1	2.65	3.06		0.096	0.096					5.8	6.5	559
1	3.06	3.75		0.093	0.093					6.3	6.5	494
1	3.75	5.3		0.092	0.092					5.8	7.3	387
1	5.3	27.12		0.067	0.067					6.9	5.4	236

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	1.675	12.627		1.56		5311	305	91.1		0.17	0.169		0.197			21.155

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]
-1.851			-6.575		-5.814

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.981
f_angle_d	0.969
f_chiral_restr	0.072
f_bond_d	0.005
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	403
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SCALA	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
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.