3TNL

1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with Shikimate and NAD.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NPDpdb entry 1NPD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295Protein: 7.5mG/mL, 0.25M Sodium chloride, 0.01M TRIS-HCl (pH 8.3), 1mM Shikimate; Screen: PEG's (D2), 0.1M HEPES (pH 7.5), 25% (w/v) PEG 4000. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1642.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.851α = 90
b = 82.878β = 90.03
c = 101.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium lenses2011-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.453096.70.05520.63.8203043203043-317.9
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)
11.451.4889.40.343.13.49339

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTpdb entry 1NPD1.4529.311926811926811015596.680.150110.150110.148710.17645RANDOM15.508
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]
-1.261.231.72-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.385
r_dihedral_angle_4_deg12.325
r_dihedral_angle_3_deg9.119
r_scangle_it4.708
r_dihedral_angle_1_deg3.872
r_scbond_it2.922
r_mcangle_it1.761
r_angle_refined_deg1.607
r_mcbond_it1.079
r_angle_other_deg0.898
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.385
r_dihedral_angle_4_deg12.325
r_dihedral_angle_3_deg9.119
r_scangle_it4.708
r_dihedral_angle_1_deg3.872
r_scbond_it2.922
r_mcangle_it1.761
r_angle_refined_deg1.607
r_mcbond_it1.079
r_angle_other_deg0.898
r_mcbond_other0.382
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8944
Nucleic Acid Atoms
Solvent Atoms1907
Heterogen Atoms204

Software

Software
Software NamePurpose
Blu-Icedata collection
BALBESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling