2PZ8 | pdb_00002pz8

NAD+ Synthetase from Bacillus anthracis with AMP-CPP and Mg2+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PZB	Bacillus anthracis NAD+ synthetase apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	10% PEG 8000, 0.505 M ammonium sulfate, 6% glycerol, 100 mM MgCl2, 0.05% n-octyl-BETA-D-glucopyranoside, 10 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.183	α = 90
b = 96.507	β = 90
c = 68.633	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	93	IMAGE PLATE	RIGAKU RAXIS IV		2006-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	37	99.9	0.088	14.9	7	48875	48827	2	2	14.4

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	2.07	99.6		0.402	3.15	6.2	4802

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	Bacillus anthracis NAD+ synthetase apo structure	2	37	2	44875	44866	4537	91.8	0.229	0.202	0.202	0.19	0.229	0.22	RANDOM	24.5

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]
-5.96			9.53		-3.57

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.4
c_scangle_it	2.83
c_scbond_it	1.95
c_mcangle_it	1.65
c_angle_deg	1.2
c_mcbond_it	1.13
c_improper_angle_d	0.77
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4360
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	76

Software

Software
Software Name	Purpose
CNS	refinement
StructureStudio	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing