1L4Y

CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AT 2.0 ANGSTROM RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L4UPDB ENTRY 1L4U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5288.2PEG 4000, Magnesium Choloride, Sodium Chloride, ADENOSINE-5'-DIPHOSPHATE, SHIKIMIC ACID, Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.2K
Crystal Properties
Matthews coefficientSolvent content
2.9157.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.86α = 90
b = 63.86β = 90
c = 92.07γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRROR1999-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9B0.92000NSLSX9B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
1227.6599.40.0390.05626.65.881511014820-326.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.90.3890.414.645.81461

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONDifference FourierTHROUGHOUTPDB ENTRY 1L4U230148201482073997.80.2170.252RANDOM35.1
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]
3.76-0.783.76-7.52
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.2
c_scangle_it4.31
c_scbond_it3.01
c_mcangle_it2.87
c_mcbond_it1.99
c_angle_deg1.2
c_improper_angle_d0.81
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1226
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms33

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing