2IYY

Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate-3-phosphate and SO4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IYXPDB ENTRY 2IYX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18200MM MGSO4, 20%(W/V) PEG 3350, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.550.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.349α = 90
b = 59.349β = 90
c = 102.867γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW6MPG/DESY, HAMBURGBW6

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
11.6219.1693.80.065.72.3125604
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)
11.621.6692.50.951.42.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2IYX1.6219.1624283132193.80.1780.1750.233RANDOM24.6
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]
1.410.71.41-2.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.038
r_dihedral_angle_4_deg16.139
r_dihedral_angle_3_deg15.153
r_scangle_it13.474
r_scbond_it10.359
r_mcangle_it6.137
r_mcbond_it6.022
r_dihedral_angle_1_deg5.697
r_angle_refined_deg1.651
r_angle_other_deg0.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.038
r_dihedral_angle_4_deg16.139
r_dihedral_angle_3_deg15.153
r_scangle_it13.474
r_scbond_it10.359
r_mcangle_it6.137
r_mcbond_it6.022
r_dihedral_angle_1_deg5.697
r_angle_refined_deg1.651
r_angle_other_deg0.905
r_symmetry_vdw_other0.283
r_nbd_refined0.219
r_nbd_other0.212
r_xyhbond_nbd_refined0.19
r_symmetry_vdw_refined0.178
r_nbtor_refined0.176
r_symmetry_hbond_refined0.167
r_chiral_restr0.102
r_nbtor_other0.085
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.004
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1258
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling