5ND5

Crystal structure of transketolase from Chlamydomonas reinhardtii in complex with TPP and Mg2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ITZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29310 % w/v PEG 6K, 5 % v/v MPD and 0.1 M MES pH 6.5-7.0 or 0.1 M HEPES pH 7.0-8.0
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 201.489α = 90
b = 75.93β = 109.99
c = 103.759γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R0.98ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.7497.5276.20.0530.05311.92.11149613-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.8264.60.240.241.7

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 REPLACEMENTTHROUGHOUT1ITZ1.7497.51109213575775.880.147150.145110.18603RANDOM17.723
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.788
r_dihedral_angle_4_deg19.888
r_dihedral_angle_3_deg15.37
r_dihedral_angle_1_deg6.683
r_long_range_B_refined4.506
r_long_range_B_other4.466
r_scangle_other3.564
r_scbond_it2.386
r_scbond_other2.386
r_mcangle_it2.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.788
r_dihedral_angle_4_deg19.888
r_dihedral_angle_3_deg15.37
r_dihedral_angle_1_deg6.683
r_long_range_B_refined4.506
r_long_range_B_other4.466
r_scangle_other3.564
r_scbond_it2.386
r_scbond_other2.386
r_mcangle_it2.017
r_mcangle_other2.017
r_angle_refined_deg1.939
r_mcbond_it1.448
r_mcbond_other1.448
r_angle_other_deg1.024
r_chiral_restr0.158
r_bond_refined_d0.019
r_gen_planes_refined0.011
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10219
Nucleic Acid Atoms
Solvent Atoms698
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing