2IYT

Shikimate kinase from Mycobacterium tuberculosis in unliganded state, open LID (conf. A)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IYSPDB ENTRY 2IYS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5170MM NA ACETATE, 15%(V/V) GLYCEROL, 25.5%(W/V) PEG 4000, 85MM TRIS-HCL PH 8.5
Crystal Properties
Matthews coefficientSolvent content
1.831.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.192α = 90
b = 44.192β = 90
c = 152.628γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2005-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.4719.7397.60.17.154.0526142
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)
11.471.5198.70.722.044

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 2IYS1.4719.7324844129897.60.1990.1970.246RANDOM20.54
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]
-0.08-0.080.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.553
r_dihedral_angle_4_deg17.585
r_scangle_it16.113
r_dihedral_angle_3_deg14.959
r_scbond_it14.15
r_mcangle_it6.532
r_dihedral_angle_1_deg5.165
r_mcbond_it4.99
r_angle_other_deg3.571
r_angle_refined_deg1.766
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.553
r_dihedral_angle_4_deg17.585
r_scangle_it16.113
r_dihedral_angle_3_deg14.959
r_scbond_it14.15
r_mcangle_it6.532
r_dihedral_angle_1_deg5.165
r_mcbond_it4.99
r_angle_other_deg3.571
r_angle_refined_deg1.766
r_symmetry_vdw_other0.332
r_nbd_other0.233
r_nbd_refined0.228
r_symmetry_vdw_refined0.228
r_symmetry_hbond_refined0.188
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.152
r_chiral_restr0.117
r_nbtor_other0.102
r_bond_refined_d0.021
r_gen_planes_other0.011
r_gen_planes_refined0.009
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 Atoms1293
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling