3M6L

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate and calcium ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M34 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.22910.2 M NaCl, 20 % PEG 1000, 0.1 M Na/K phosphate, 10mM TPP, 10 mM R5P, 1mM CaCl2, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1843.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.924α = 90
b = 71.462β = 109.48
c = 69.617γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2010-02-10MSINGLE 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
11.594094.80.085193.880420765881.9227
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)
11.591.6372.10.741.93.42898

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 REPLACEMENTTHROUGHOUT3M341.59401.97649872677382194.280.180.161730.159680.20086RANDOM15.947
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]
-0.521.831.060.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.2
r_dihedral_angle_4_deg14.355
r_dihedral_angle_3_deg14.111
r_dihedral_angle_1_deg6.065
r_scangle_it5.794
r_scbond_it3.709
r_mcangle_it2.241
r_angle_refined_deg2.17
r_mcbond_it1.404
r_angle_other_deg1.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.2
r_dihedral_angle_4_deg14.355
r_dihedral_angle_3_deg14.111
r_dihedral_angle_1_deg6.065
r_scangle_it5.794
r_scbond_it3.709
r_mcangle_it2.241
r_angle_refined_deg2.17
r_mcbond_it1.404
r_angle_other_deg1.122
r_mcbond_other0.486
r_chiral_restr0.14
r_bond_refined_d0.022
r_gen_planes_refined0.012
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 Atoms565
Heterogen Atoms56

Software

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