2DFT

Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and Mg at 2.8 angstrons of resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WE2PDB ENTRY 1WE2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION82930,1M tris HCl, pH 8.0, 25% PEG 3350 and 0,1M MgCl2, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1643.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.619α = 90
b = 62.203β = 90
c = 170.633γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2005-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.427LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.863.2599.65.7171301705722
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.9519.07

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1WE22.857.172165481567083299.720.188060.1830.182940.28162RANDOM34.155
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]
0.54-0.11-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.772
r_dihedral_angle_3_deg22.639
r_dihedral_angle_4_deg22.3
r_dihedral_angle_1_deg11.859
r_scangle_it11.064
r_scbond_it10.281
r_mcbond_it7.936
r_mcangle_it7.517
r_angle_refined_deg3.754
r_symmetry_hbond_refined0.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.772
r_dihedral_angle_3_deg22.639
r_dihedral_angle_4_deg22.3
r_dihedral_angle_1_deg11.859
r_scangle_it11.064
r_scbond_it10.281
r_mcbond_it7.936
r_mcangle_it7.517
r_angle_refined_deg3.754
r_symmetry_hbond_refined0.446
r_symmetry_vdw_refined0.419
r_nbtor_refined0.353
r_nbd_refined0.343
r_xyhbond_nbd_refined0.282
r_chiral_restr0.242
r_metal_ion_refined0.174
r_bond_refined_d0.029
r_gen_planes_refined0.023
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4777
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing