3MMO | pdb_00003mmo

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OT4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	278	Protein solution (5mcl): 14.5mg/ml TvNiR, 0.05M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG 400. Crystal was soaked in 0.1M KCN for 1h, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Properties
Matthews coefficient	Solvent content
4.23	70.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 194.56	α = 90
b = 194.56	β = 90
c = 194.56	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		2004-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.81	EMBL/DESY, HAMBURG	X11

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	1.55	12	99.9	0.047	40.1	4.9	350567	350257			25.1

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	1.55	1.57	100		0.421	3.9	4.8	11650

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	2OT4	1.55	11.98	332621	17636	99.66	0.14878	0.1481	0.16	0.16175	0.17	RANDOM	18.046

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	36.292
r_dihedral_angle_4_deg	18.014
r_dihedral_angle_3_deg	11.815
r_dihedral_angle_1_deg	6.109
r_scangle_it	3.228
r_scbond_it	2.138
r_angle_refined_deg	1.609
r_mcangle_it	1.497
r_angle_other_deg	0.977
r_mcbond_it	0.904

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.292
r_dihedral_angle_4_deg	18.014
r_dihedral_angle_3_deg	11.815
r_dihedral_angle_1_deg	6.109
r_scangle_it	3.228
r_scbond_it	2.138
r_angle_refined_deg	1.609
r_mcangle_it	1.497
r_angle_other_deg	0.977
r_mcbond_it	0.904
r_mcbond_other	0.249
r_chiral_restr	0.097
r_bond_refined_d	0.02
r_gen_planes_refined	0.016
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8217
Nucleic Acid Atoms
Solvent Atoms	1218
Heterogen Atoms	826

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.