1IH8

NH3-dependent NAD+ Synthetase from Bacillus subtilis Complexed with AMP-CPP and Mg2+ ions.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NSYpdb entry 1NSY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5295VAPOR DIFFUSION IN MICROSEEDED HANGING DROPS. 20-26% PEG400, 0.05 M HEPES SODIUM SALT, PH=7.5, 0.1 M MAGNESIUM CHLORIDE, 0.002 M AMP-CPP., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.139

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.599α = 90
b = 85.411β = 110.88
c = 60.253γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMACSCIENCE DIP100mirrors2000-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.93098.80.04820.42.911288438796-1010.8
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)
1.91.9798.40.1547.62.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 1NSY1.929.831.3623879637901190096.40.1750.1670.1670.205RANDOM15.4
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]
-0.721.46-0.321.05
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.1
c_scangle_it3
c_scbond_it2.03
c_mcangle_it1.7
c_mcbond_it1.17
c_angle_deg1.1
c_improper_angle_d0.71
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4072
Nucleic Acid Atoms
Solvent Atoms590
Heterogen Atoms34

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing