3X1N | pdb_00003x1n

Nitrite-bound thermostable copper nitrite reductase at 320 K

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	5.5% PEG 4000, 0.1M sodium acetate, 0.075M copper sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.3	α = 90
b = 116.3	β = 90
c = 85.652	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	320	CCD	ADSC QUANTUM 315		2013-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.00000	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	50	96.6	0.066		3.9		60565

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	98.9		0.377	2.5	3.7

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	3WKO	1.55	34.79	57494	3063	96.6	0.11539	0.11454	0.13	0.13141	0.14	RANDOM	24.242

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	43.907
r_dihedral_angle_3_deg	14.787
r_dihedral_angle_4_deg	13.597
r_dihedral_angle_1_deg	7.851
r_long_range_B_refined	6.409
r_sphericity_bonded	6.393
r_long_range_B_other	6.284
r_scangle_other	5.067
r_scbond_it	3.432
r_scbond_other	3.395
r_mcangle_it	2.899
r_mcangle_other	2.898
r_angle_refined_deg	2.365
r_mcbond_it	2.064
r_mcbond_other	2.064
r_angle_other_deg	0.947
r_chiral_restr	0.142
r_bond_refined_d	0.025
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2313
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	9

Software

Software
Software Name	Purpose
BSS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling