2IYX

Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate and SO4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IYQPDB ENTRY 2IYQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18200MM MGSO4, 20%(W/V) PEG 3350, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.550.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.245α = 90
b = 59.245β = 90
c = 102.797γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-08-07MSINGLE 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
11.4919.5199.40.0412.693.0434443
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)
11.491.5398.70.412.173

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 2IYQ1.4919.5132698174699.40.1680.1670.206RANDOM18.75
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]
1.050.521.05-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.549
r_dihedral_angle_4_deg15.013
r_dihedral_angle_3_deg13.524
r_scangle_it13.519
r_scbond_it10.804
r_mcbond_it6.397
r_mcangle_it6.231
r_dihedral_angle_1_deg5.317
r_angle_refined_deg1.795
r_angle_other_deg0.942
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.549
r_dihedral_angle_4_deg15.013
r_dihedral_angle_3_deg13.524
r_scangle_it13.519
r_scbond_it10.804
r_mcbond_it6.397
r_mcangle_it6.231
r_dihedral_angle_1_deg5.317
r_angle_refined_deg1.795
r_angle_other_deg0.942
r_symmetry_vdw_other0.297
r_symmetry_vdw_refined0.241
r_nbd_refined0.237
r_nbd_other0.206
r_symmetry_hbond_refined0.182
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.162
r_chiral_restr0.106
r_nbtor_other0.083
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.002
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 Atoms1253
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing