3M34

Crystal structure of transketolase in complex with thiamin diphosphate and calcium ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L84 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.52930.1 M Ches ph 9.5 30 % PEG 400 10 mM TPP, 1mm CaCl2. Sitting drop, vapor diffusion method Temp 293 K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1342.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.35α = 90
b = 70.819β = 109.92
c = 69.236γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2009-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

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
11.654099.40.0817.63.670630705902231.4
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)
11.651.6899.90.612.23.53508

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT3L841.6540227060067019356699.240.170.152940.151410.18186RANDOM19.448
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]
0.460.110.56-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.025
r_dihedral_angle_3_deg12.905
r_dihedral_angle_4_deg12.636
r_dihedral_angle_1_deg6.041
r_scangle_it5.023
r_scbond_it3.064
r_angle_refined_deg1.809
r_mcangle_it1.793
r_mcbond_it1.037
r_angle_other_deg0.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.025
r_dihedral_angle_3_deg12.905
r_dihedral_angle_4_deg12.636
r_dihedral_angle_1_deg6.041
r_scangle_it5.023
r_scbond_it3.064
r_angle_refined_deg1.809
r_mcangle_it1.793
r_mcbond_it1.037
r_angle_other_deg0.976
r_mcbond_other0.345
r_chiral_restr0.161
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4901
Nucleic Acid Atoms
Solvent Atoms420
Heterogen Atoms43

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling