3P52 | pdb_00003p52

NH3-dependent NAD synthetase from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with the nitrate ion

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	4.25 M NaNitrate, 0.1 M Bis-Tris, 10 mM NAD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.945	α = 90
b = 120.945	β = 90
c = 91.795	γ = 120

Symmetry
Space Group	P 3 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	MARMOSAIC 300 mm CCD	MIRROR	2010-07-31	M	MOLECULAR REPLACEMENT

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

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	2.74	30	100	0.076	23.2	7.6	20690	20690		-3	74

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)
	2.74	2.8	100		0.882	2.3	7.7	1029

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1XNH	2.74	30	19563	19563	1056	99.21	0.21084	0.20911	0.21	0.24451	0.24	RANDOM	72.083

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]
1.27	0.64		1.27		-1.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.761
r_dihedral_angle_4_deg	20.196
r_dihedral_angle_3_deg	19.143
r_dihedral_angle_1_deg	5.218
r_scangle_it	4.636
r_scbond_it	2.97
r_angle_refined_deg	1.653
r_mcangle_it	1.475
r_mcbond_it	0.72
r_chiral_restr	0.11
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3577
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	16

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
CCP4	model building
MrBUMP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
CCP4	phasing