2PZ8

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727710% 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 coefficientSolvent content
2.8156.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.183α = 90
b = 96.507β = 90
c = 68.633γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV2006-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
123799.90.08814.9748875488272214.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.60.4023.156.24802

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTBacillus anthracis NAD+ synthetase apo structure23724487544866453791.80.2290.2020.2020.229RANDOM24.5
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]
-5.969.53-3.57
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.4
c_scangle_it2.83
c_scbond_it1.95
c_mcangle_it1.65
c_angle_deg1.2
c_mcbond_it1.13
c_improper_angle_d0.77
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.4
c_scangle_it2.83
c_scbond_it1.95
c_mcangle_it1.65
c_angle_deg1.2
c_mcbond_it1.13
c_improper_angle_d0.77
c_bond_d0.007
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 AtomsNumber
Protein Atoms4360
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms76

Software

Software
Software NamePurpose
CNSrefinement
StructureStudiodata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing