3B6J | pdb_00003b6j

WrbA from Escherichia coli, NADH complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B6I	PDB entry 3B6I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	293	15-35 % PEG 1500, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.62	73.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.2	α = 90
b = 94.2	β = 90
c = 173.644	γ = 90

Symmetry
Space Group	P 43 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	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2007-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.05	50	96.9	0.12	5.9	4.1	49693	48152	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.15	93.7		0.5	1.9	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	PDB entry 3B6I	2.05	49.32	2	2	49693	45683	2441	96.7	0.16991	0.16833	0.1671	0.19936	0.1981	RANDOM	34.223

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]
0.64			0.64		-1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.589
r_dihedral_angle_4_deg	21.001
r_dihedral_angle_3_deg	15.014
r_dihedral_angle_1_deg	5.894
r_scangle_it	3.968
r_scbond_it	2.486
r_angle_refined_deg	2.046
r_mcangle_it	1.45
r_mcbond_it	0.96
r_nbtor_refined	0.303
r_symmetry_hbond_refined	0.242
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.211
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.109
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2916
Nucleic Acid Atoms
Solvent Atoms	361
Heterogen Atoms	264

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing