3QVD | pdb_00003qvd

Exposure of rubrerythrin from Pyrococcus furiosus to peroxide, fifteen second time point.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Capillary batch	7.2	298	Performed in an anaerobic chamber with less than 1 ppm oxygen at all times. 0.02 M TRIS, 30% PEG 2K MME, pH 7.2, Capillary batch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.589	α = 90
b = 104.458	β = 90.51
c = 104.512	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	115	IMAGE PLATE	MAR scanner 345 mm plate		2010-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	2	50	96.7	0.1	0.09	21.9	4.1	115349	111550	2	2	26.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	46.73	115349	111550	5629	96.7	0.211	0.211	0.2	0.235	0.23	RANDOM	39.3

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]
11.12		0.01	-5.76		-5.36

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.9
c_scangle_it	3.39
c_scbond_it	2.25
c_mcangle_it	1.78
c_mcbond_it	1.23
c_angle_deg	1.1
c_improper_angle_d	0.69
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10904
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	36

Software

Software
Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

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.