5AI2 | pdb_00005ai2

Anomalous Neutron phased crystal structure of 113Cd-substituted Perdeuterated Pyrococcus furiosus rubredoxin to 1.75A resolution at 295K

NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.44	α = 90
b = 34.14	β = 90
c = 43.78	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	295	5ATM 3HE, CURVED 120X30 DEGREES	INSTITUT LAUE LANGEVIN DETECTOR GROUP	BORON CARBIDE BEAM DEFINING APERTURE	2014-12-01

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ILL		ILL	D19

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	1.75	34.44	99.9	0.14	0.04		13.4		5560		2	8.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.84	99.9		0.457	0.149	5.4	10.6

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	EXPERIMENTAL ANOMALOUS NEUTRON PHASING	NONE	1.75	27.068	1.34	10050	451	99.81	0.2357	0.2331	0.2864

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	14.246
f_angle_d	0.613
f_chiral_restr	0.024
f_bond_d	0.003
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	421
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
SHELXCD	phasing
SHELXE	phasing
RETREAT	data reduction
RETREAT	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.