2IYZ

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18200MM NH4F,20%(W/V) PEG 3350, pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.551.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.61α = 90
b = 59.61β = 90
c = 102.911γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-02-26MSINGLE 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
12.319.4995.80.096.691.969427
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)
12.32.3698.70.32.791.9

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 2IYX2.319.49897844995.80.1930.1910.242RANDOM24.47
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]
1.250.631.25-1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.065
r_dihedral_angle_3_deg15.778
r_dihedral_angle_4_deg14.025
r_dihedral_angle_1_deg5.087
r_scangle_it3.214
r_scbond_it2.018
r_angle_refined_deg1.526
r_mcangle_it1.185
r_mcbond_it1.106
r_angle_other_deg0.815
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.065
r_dihedral_angle_3_deg15.778
r_dihedral_angle_4_deg14.025
r_dihedral_angle_1_deg5.087
r_scangle_it3.214
r_scbond_it2.018
r_angle_refined_deg1.526
r_mcangle_it1.185
r_mcbond_it1.106
r_angle_other_deg0.815
r_symmetry_vdw_other0.244
r_nbd_refined0.214
r_nbd_other0.193
r_symmetry_hbond_refined0.193
r_xyhbond_nbd_refined0.185
r_nbtor_refined0.168
r_symmetry_vdw_refined0.148
r_nbtor_other0.083
r_chiral_restr0.072
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1247
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling