1NDT

NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AFN	PDB ENTRY 1AFN MONOMER

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		pH 4.60

Crystal Properties
Matthews coefficient	Solvent content
2.64	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.236	α = 90
b = 81.236	β = 90
c = 100.034	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MARRESEARCH	TORROIDAL MIRROR	1996-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.5		SRS	PX9.5

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	2.1	70.4	98.6	0.073	9.4	4.5		21904			18.4

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	2.1	2.15	99.3		0.307	2.3	4.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT, EXCEPT FINAL CYCLE	PDB ENTRY 1AFN MONOMER	2.1	20	20483	1099	99.7	0.164	0.167	0.208	RANDOM	19.9

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
p_transverse_tor	25
p_staggered_tor	15
p_special_tor	15
p_planar_tor	7
p_mcangle_it	3
p_scangle_it	3
p_mcbond_it	2
p_scbond_it	2
p_singtor_nbd	0.3
p_multtor_nbd	0.3
p_xhyhbond_nbd	0.3
p_xyhbond_nbd	0.3
p_chiral_restr	0.15
p_planar_d	0.05
p_hb_or_metal_coord	0.05
p_angle_d	0.04
p_plane_restr	0.03
p_bond_d	0.02
p_angle_deg
p_orthonormal_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2539
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	3

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling