2JIM | pdb_00002jim

A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NAP	PDB ENTRY 2NAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		COCRYSTALLISATION WITH 10MM OF NAN3 (AZIDE) IN 200MM OF DDNAPA (IE PROTEIN) WHICH HAD BEEN REDUCED BY DITHIONITE IN ANAEROBIC CONDITIONS AND THEN AIR REOXIDISED BEFORE SETTTING UP FOR CRYSTALLISATIONS STRAIGHT AFTER THAWING FROM 193K. CRYSTALLISATION CONDITION 0.1M MES PH 6.0, 8% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.307	α = 90
b = 106.307	β = 90
c = 133.558	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD		2004-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	2.45	54.07	99.9	0.13	18.1	9.8		32649		1

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	2.45	2.58	99.8		1.16	1	5.8

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	PDB ENTRY 2NAP	2.45	92.06	31238	1300	99.7	0.181	0.178	0.19	0.252	0.26	RANDOM	47.87

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]
-2.39	-1.2		-2.39		3.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.749
r_dihedral_angle_4_deg	23.346
r_dihedral_angle_3_deg	18.121
r_dihedral_angle_1_deg	6.758
r_scangle_it	2.911
r_scbond_it	1.858
r_angle_refined_deg	1.67
r_mcangle_it	1.079
r_mcbond_it	0.633
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.283
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.213
r_symmetry_vdw_refined	0.168
r_chiral_restr	0.112
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5622
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	phasing