1NDS | pdb_00001nds

CRYSTALLOGRAPHIC STRUCTURE OF A SUBSTRATE BOUND BLUE COPPER 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	NITRITE REDUCTASE PDB CODE 1AFN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6	277	28% PEG 4000, 0.1M SODIUM ACETATE, PH 4.6, 4 DEGREES C, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.89	α = 90
b = 102.2	β = 90
c = 151.88	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	286	IMAGE PLATE	MARRESEARCH	FOCUSSING PLATINUM COATED : TORROID	1996-04-24	M

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	2.8	53	91.9	0.053	9.3	3.1		24358			17.2

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)
	2.8	2.87	82.5		0.101	6.3	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	R-FREE	NITRITE REDUCTASE PDB CODE 1AFN	2.8	8	2	24342	1138	90.2	0.236	0.236	0.5	0.28	RANDOM	10.9

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
x_dihedral_angle_d	27.4
x_angle_deg	2.8
x_improper_angle_d	1.5
x_bond_d	0.022
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_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7278
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	15

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling
X-PLOR	phasing