3MPS | pdb_00003mps

Peroxide Bound Oxidized Rubrerythrin from Pyrococcus furiosus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	297	0.1M Bis-Tris, 28% w/v polyethylene glycol monomethyl ether 2,000 , pH 6.5, EVAPORATION, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.398	α = 90
b = 105.164	β = 90.13
c = 105.22	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		CCD	MARMOSAIC 300 mm CCD	Si 220. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.54	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	105.41	99.58	0.121		7		117636		6.2

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 (All)	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	105.41	117636	5897	99.58	0.245	0.245	0.242	0.2422	0.291	0.2906	RANDOM	24.062

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]
1.51		-0.16	-0.59		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.57
r_dihedral_angle_4_deg	20.185
r_dihedral_angle_3_deg	17.28
r_dihedral_angle_1_deg	5.473
r_scangle_it	2.42
r_scbond_it	1.604
r_angle_refined_deg	1.215
r_mcangle_it	0.917
r_mcbond_it	0.577
r_nbtor_refined	0.303
r_symmetry_hbond_refined	0.261
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.084
r_metal_ion_refined	0.017
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10844
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	30

Software

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