3UU9 | pdb_00003uu9

Structure of the free TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LGQ	PDB ENTRY 3LGQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	278	2.5 uL protein solution (11.6 mg/mL TvNiR in 0.02 M sodium tetraborate, 0.05 M Tris-HCl, pH 8.0) + 2.5 uL reservoir solution (0.2 M trisodium citrate, 0.1 M Tris-HCl, pH 8.5, 30% v/v PEG400, 0.1 M hydroxylamine), VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
4.96	75.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 191.387	α = 90
b = 191.387	β = 90
c = 191.387	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2010-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.978	KURCHATOV SNC	K4.4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	135.331	99.8	0.139	9.9		117913	117676			37

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.5	99.7		0.616	2.8		37149

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 3LGQ	2.2	100	111744	5897	99.81	0.15796	0.15659	0.1594	0.18433	0.1872	RANDOM	34.86

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	36.629
r_dihedral_angle_4_deg	18.742
r_dihedral_angle_3_deg	13.385
r_dihedral_angle_1_deg	6.517
r_scangle_it	3.586
r_scbond_it	2.467
r_angle_refined_deg	1.596
r_mcangle_it	1.411
r_mcbond_it	0.774
r_chiral_restr	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8225
Nucleic Acid Atoms
Solvent Atoms	900
Heterogen Atoms	787

Software

Software
Software Name	Purpose
AUTOMAR	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling