3NN1 | pdb_00003nn1

Structure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with imidazole

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		IN-HOUSE MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	1.4M sodium/potassium phosphate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.67	α = 90
b = 145.67	β = 90
c = 136.44	γ = 120

Symmetry
Space Group	P 32 2 1

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	ADSC QUANTUM 4		2008-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	126	97			276446	268021

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.85	1.9	90.7

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	IN-HOUSE MODEL	1.85	47.68	134596	134596	7117	99.7	0.18148	0.18148	0.17998	0.18	0.20988	0.21	RANDOM	32.5

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]
-0.39	-0.19		-0.39		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.047
r_dihedral_angle_4_deg	19.327
r_dihedral_angle_3_deg	14.412
r_dihedral_angle_1_deg	5.89
r_scangle_it	3.023
r_angle_other_deg	2.187
r_scbond_it	1.986
r_angle_refined_deg	1.399
r_mcangle_it	1.255
r_mcbond_it	0.721

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.047
r_dihedral_angle_4_deg	19.327
r_dihedral_angle_3_deg	14.412
r_dihedral_angle_1_deg	5.89
r_scangle_it	3.023
r_angle_other_deg	2.187
r_scbond_it	1.986
r_angle_refined_deg	1.399
r_mcangle_it	1.255
r_mcbond_it	0.721
r_mcbond_other	0.118
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9595
Nucleic Acid Atoms
Solvent Atoms	913
Heterogen Atoms	351

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	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.