1SJM | pdb_00001sjm

Nitrite bound copper containing nitrite reductase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J9Q	PDB entry 1J9Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	PEG 4000, sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 321K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.6	α = 90
b = 102.45	β = 90
c = 145.98	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2002-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.08	SSRL	BL7-1

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	1.4	25	97.3	0.041	21	7.3	1173705	1173705

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)
	1.4	1.45	93.4		0.121

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1J9Q	1.4	24.85	167035	9856	100	0.11465	0.11326	0.13846	RANDOM	12.49

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]
0.03			-0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.331
r_scangle_it	3.785
r_scbond_it	2.52
r_mcangle_it	1.616
r_angle_refined_deg	1.398
r_mcbond_it	1.063
r_angle_other_deg	0.802
r_symmetry_vdw_other	0.268
r_symmetry_vdw_refined	0.255
r_nbd_other	0.252
r_nbd_refined	0.204
r_symmetry_hbond_refined	0.202
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.09
r_nbtor_other	0.08
r_gen_planes_other	0.016
r_gen_planes_refined	0.011
r_bond_refined_d	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7708
Nucleic Acid Atoms
Solvent Atoms	1144
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling