3NN4 | pdb_00003nn4

Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant

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	4	295	0.4-0.6M ammonium sulphate, 0.1M citric acid, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.41	α = 90
b = 113.88	β = 118.02
c = 119.87	γ = 90

Symmetry
Space Group	C 1 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 210		2009-06-24	M	SINGLE WAVELENGTH

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

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	2.7	106	91.5				44825

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.77	80.9

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	2.7	43.72	42510	42510	2256	99.84	0.21831	0.21831	0.21609	0.22	0.25798	0.27	RANDOM	77.041

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]
-0.3		-8.42	-2.13		-5.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.342
r_dihedral_angle_4_deg	19.801
r_dihedral_angle_3_deg	18.062
r_dihedral_angle_1_deg	5.568
r_scangle_it	1.694
r_angle_refined_deg	1.325
r_scbond_it	1.162
r_angle_other_deg	0.909
r_mcangle_it	0.574
r_mcbond_it	0.457
r_symmetry_hbond_refined	0.4
r_symmetry_vdw_refined	0.254
r_symmetry_vdw_other	0.253
r_nbd_refined	0.211
r_mcbond_other	0.21
r_nbd_other	0.191
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.175
r_xyhbond_nbd_other	0.144
r_nbtor_other	0.086
r_chiral_restr	0.071
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9585
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	320

Software

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