1NIR | pdb_00001nir

OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		unpublished NITRITE REDUCTASE FROM THIOSPHAERA PANTOTROPHA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.4		PROTEIN WAS CRYSTALLIZED FROM @M NA/K2 PHOSPHATE, 50MM TRIS-HCL, PH 8.4

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.068	α = 90
b = 90.072	β = 90
c = 111.888	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	X RAY IMAGE INTENSIFIER (THOMPSON) +PRINCETON CCD DETECTOR	THOMPSON	FOCUSED BEAM TOROIDAL MIRROR	1997-01-31	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID09		ESRF	ID09

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.15	30	99.3	0.063	0.063	7.7	3.8		91663		2	36.18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.15	2.27	96.9		0.214	0.214	3.4	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	2.15	30	2.5	82362	2937	89	0.209	0.209	0.32	0.242	0.33	RANDOM	39.1

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]
3.2			3.416		3.18

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	26.59
x_scbond_it	3.2
x_mcbond_it	2
x_angle_deg	1.857
x_improper_angle_d	1.342
x_bond_d	0.014
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcangle_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8415
Nucleic Acid Atoms
Solvent Atoms	870
Heterogen Atoms	198

Software

Software
Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
PROW	data reduction
CCP4	data scaling