1NPD

X-RAY STRUCTURE OF SHIKIMATE DEHYDROGENASE COMPLEXED WITH NAD+ FROM E.COLI (YDIB) NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER24


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2294200mM ammonium acetate, 100mM tri-sodium citrate dihydrate, 25% PEG 6000, pH 5.2, temperature 294K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1241.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.185α = 90
b = 157.185β = 90
c = 39.782γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDBRANDEIS - B42002-11-22MMULTIPLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C0.979, 0.9787, 0.92NSLSX12C

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
12.310099.80.09231.210.9348734-331.7
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)
2.32.370.3735.314088

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.319.711125464247341260970.2170.2170.274RANDOM35
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]
-1.154.56-1.152.3
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.7
c_scangle_it3.55
c_scbond_it2.5
c_mcangle_it2.34
c_mcbond_it1.45
c_angle_deg1.3
c_improper_angle_d0.93
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.7
c_scangle_it3.55
c_scbond_it2.5
c_mcangle_it2.34
c_mcbond_it1.45
c_angle_deg1.3
c_improper_angle_d0.93
c_bond_d0.009
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 Atoms4374
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms88

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing