2IYV

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.525%(W/V) PEG 3000, 100MM MES PH 6.5
Crystal Properties
Matthews coefficientSolvent content
237.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.618α = 90
b = 44.193β = 109.13
c = 51.289γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2001-07-12MSINGLE 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
11.3519.2897.20.077.352.5134977
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)
11.351.3892.80.571.642.4

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 2IYQ1.3519.2833221175697.20.140.1380.178RANDOM14.5
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]
1.980.84-0.97-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.377
r_dihedral_angle_4_deg15.859
r_dihedral_angle_3_deg13.489
r_scangle_it6.689
r_scbond_it5.07
r_dihedral_angle_1_deg5.055
r_mcangle_it4.525
r_mcbond_it4.098
r_angle_refined_deg1.517
r_angle_other_deg0.845
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.377
r_dihedral_angle_4_deg15.859
r_dihedral_angle_3_deg13.489
r_scangle_it6.689
r_scbond_it5.07
r_dihedral_angle_1_deg5.055
r_mcangle_it4.525
r_mcbond_it4.098
r_angle_refined_deg1.517
r_angle_other_deg0.845
r_symmetry_vdw_other0.244
r_nbd_refined0.232
r_nbd_other0.203
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.155
r_symmetry_vdw_refined0.138
r_chiral_restr0.09
r_nbtor_other0.082
r_symmetry_hbond_refined0.077
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms1334
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing