3PZA | pdb_00003pza

Fully Reduced (All-ferrous) Pyrococcus rubrerythrin after a 10 second exposure to peroxide.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Capillary batch	7	291	0.025 M HEPES pH 7.0, 8% PEG 2000 MME, Capillary batch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.602	α = 90
b = 104.602	β = 90
c = 79.591	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MAR CCD 165 mm	1.0	2010-11-21	M	SINGLE WAVELENGTH

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

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	1.85	50	99.4	0.101	0.082	42	6	38239	38044	2	2

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.85	43.71	38044	1941	99.49	0.1768	0.1756	0.17	0.1998	0.2	RANDOM	26.457

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]
-0.2			-0.2		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.021
r_dihedral_angle_4_deg	14.984
r_dihedral_angle_3_deg	14.707
r_scangle_it	8.063
r_dihedral_angle_1_deg	5.234
r_scbond_it	4.714
r_mcangle_it	2.634
r_angle_refined_deg	2.239
r_mcbond_it	1.534
r_chiral_restr	0.176
r_bond_refined_d	0.035
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2726
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	10

Software

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