2P0B | pdb_00002p0b

Crystal structure of chemically-reduced E.coli nrfB

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OZY	OXIDISED STRUCTURE OF NRFB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	289	Purified NrfB was concentrated to 8 mg/ml before crystallization. Crystals were obtained by the vapour diffusion method under anaerobic conditions using 250 mM tri-sodium citrate, 10 mM Na2S2O4 and 20 % (v/v) isopropanol in 100 mM sodium HEPES pH 7.5. Crystals were soaked in 100 mM Na2S2O4 prior to harvesting, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.727	α = 90
b = 59.433	β = 90
c = 65.318	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		CCD	ADSC QUANTUM 315		2006-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.74	43.98	94	0.131	0.131	4.7	4.2		19070			8.46

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	1.74	1.83	97		0.433	0.433	1.5	4	2846

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	OXIDISED STRUCTURE OF NRFB	1.74	7.99	18843	18843	957	93.16	0.161	0.161	0.159	0.16	0.192	0.19	RANDOM	10.925

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
r_dihedral_angle_2_deg	35.1
r_dihedral_angle_4_deg	22.656
r_dihedral_angle_3_deg	12.667
r_dihedral_angle_1_deg	5.523
r_scangle_it	2.88
r_scbond_it	1.88
r_angle_refined_deg	1.577
r_mcangle_it	1.25
r_mcbond_it	0.772
r_nbd_refined	0.355
r_nbtor_refined	0.295
r_symmetry_vdw_refined	0.18
r_symmetry_hbond_refined	0.127
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.099
r_metal_ion_refined	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1099
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	215

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
MOLREP	phasing