3M7I

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate(pyranose form) and magnesium ion


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5.2 M NaCl 30% Peg 400 0.1 M HEPES 10 mM RP5, 10 mM TPP, 1mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1442.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.337α = 90
b = 70.955β = 109.4
c = 69.189γ = 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
11.754097.50.09412.73.259272578272234.3
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)
11.751.7899.90.4153.22.92940

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 REPLACEMENTTHROUGHOUT3M341.7540225781654908290896.760.1940.171210.167110.21076RANDOM23.719
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]
-0.540.961.030.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.646
r_dihedral_angle_4_deg15.121
r_dihedral_angle_3_deg13.709
r_dihedral_angle_1_deg6.101
r_scangle_it5.043
r_scbond_it3.136
r_mcangle_it1.893
r_angle_refined_deg1.858
r_mcbond_it1.11
r_angle_other_deg1.024
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.646
r_dihedral_angle_4_deg15.121
r_dihedral_angle_3_deg13.709
r_dihedral_angle_1_deg6.101
r_scangle_it5.043
r_scbond_it3.136
r_mcangle_it1.893
r_angle_refined_deg1.858
r_mcbond_it1.11
r_angle_other_deg1.024
r_mcbond_other0.367
r_chiral_restr0.114
r_bond_refined_d0.022
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 Atoms328
Heterogen Atoms45

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
Cootmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing