6YAK

Split gene transketolase, active alpha2beta2 heterotetramer


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2912.1 M DL-malic acid pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.3748.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.078α = 90
b = 130.047β = 90
c = 165.897γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9200DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.3460.87897.70.056116.46.128814923.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.341.3681.31.6190.2660.83.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1qgd1.3460.872881451440297.5840.1420.14090.158820.5
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]
-0.4160.42-0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.432
r_dihedral_angle_4_deg20.198
r_dihedral_angle_3_deg13.682
r_lrange_it7.705
r_lrange_other7.705
r_dihedral_angle_1_deg6.322
r_scangle_it5.931
r_scangle_other5.931
r_scbond_it4.231
r_scbond_other4.227
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.432
r_dihedral_angle_4_deg20.198
r_dihedral_angle_3_deg13.682
r_lrange_it7.705
r_lrange_other7.705
r_dihedral_angle_1_deg6.322
r_scangle_it5.931
r_scangle_other5.931
r_scbond_it4.231
r_scbond_other4.227
r_mcangle_it3.095
r_mcangle_other3.095
r_angle_other_deg2.27
r_mcbond_it2.261
r_mcbond_other2.26
r_angle_refined_deg1.534
r_nbd_other0.277
r_symmetry_nbd_refined0.269
r_nbd_refined0.214
r_symmetry_nbd_other0.206
r_symmetry_xyhbond_nbd_refined0.206
r_xyhbond_nbd_refined0.172
r_nbtor_refined0.161
r_symmetry_xyhbond_nbd_other0.134
r_ncsr_local_group_20.093
r_chiral_restr0.08
r_ncsr_local_group_10.078
r_symmetry_nbtor_other0.065
r_metal_ion_refined0.048
r_bond_other_d0.033
r_gen_planes_other0.013
r_bond_refined_d0.008
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8982
Nucleic Acid Atoms
Solvent Atoms1424
Heterogen Atoms204

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
MOLREPphasing
MoRDaphasing