2IYW

Shikimate kinase from Mycobacterium tuberculosis in complex with MgATP, open LID (conf. B)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.525%(W/V) PEG 3000, 100MM MES PH 6.5
Crystal Properties
Matthews coefficientSolvent content
239.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.97α = 90
b = 44.581β = 109.7
c = 51.762γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-08-24MSINGLE 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
11.8519.4798.30.09810.863.5514156
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)
11.851.9998.50.423.353.5

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 2IYV1.8519.471342273498.30.1630.1610.2RANDOM17.05
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]
0.620.64-0.390.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.55
r_dihedral_angle_4_deg15.487
r_dihedral_angle_3_deg12.395
r_scangle_it5.389
r_dihedral_angle_1_deg4.708
r_angle_other_deg3.542
r_scbond_it3.19
r_mcangle_it2.002
r_angle_refined_deg1.322
r_mcbond_it1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.55
r_dihedral_angle_4_deg15.487
r_dihedral_angle_3_deg12.395
r_scangle_it5.389
r_dihedral_angle_1_deg4.708
r_angle_other_deg3.542
r_scbond_it3.19
r_mcangle_it2.002
r_angle_refined_deg1.322
r_mcbond_it1.12
r_symmetry_vdw_other0.257
r_nbd_other0.238
r_nbd_refined0.218
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.151
r_symmetry_vdw_refined0.14
r_symmetry_hbond_refined0.131
r_nbtor_other0.1
r_chiral_restr0.066
r_bond_refined_d0.01
r_gen_planes_other0.005
r_gen_planes_refined0.004
r_bond_other_d
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 Atoms1318
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling