3GM6

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	278	Protein solution (2.5mcl): 9.3mg/ml TvNiR, 0.1M potassium phosphate (pH7.0). Reservoir solution (2.5mcl): 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 30% v/v 2-methyl-2,4-pentanediol (pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
4.49	72.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 196.56	α = 90
b = 196.56	β = 90
c = 196.56	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		2007-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.998	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	1.8	19.9	97.8	0.096	10			226620

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)
	1.79	1.85	99.8		0.229	4.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2OT4	1.8	19.9	215207	11413	97.7	0.1593	0.15862	0.172	RANDOM	18.146

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	36.191
r_dihedral_angle_4_deg	17.434
r_dihedral_angle_3_deg	12.348
r_dihedral_angle_1_deg	5.895
r_scangle_it	2.742
r_scbond_it	1.932
r_angle_refined_deg	1.529
r_mcangle_it	1.2
r_angle_other_deg	1.006
r_mcbond_it	0.859
r_symmetry_vdw_other	0.258
r_mcbond_other	0.235
r_nbd_refined	0.216
r_nbd_other	0.204
r_nbtor_refined	0.188
r_symmetry_vdw_refined	0.129
r_nbtor_other	0.106
r_symmetry_hbond_refined	0.1
r_xyhbond_nbd_refined	0.099
r_chiral_restr	0.098
r_metal_ion_refined	0.027
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8226
Nucleic Acid Atoms
Solvent Atoms	1038
Heterogen Atoms	732

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling