6YAJ

Split gene transketolase, inactive beta4 tetramer


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH291ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.9658.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.878α = 90
b = 101.878β = 90
c = 164.546γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

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
11.986.6299.80.0530.99913.15.2131289
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)
11.91.934.2450.339

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-VALUE1qgd1.964.008131176661399.7570.1790.17760.207759.984
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]
2.1672.167-4.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.746
r_dihedral_angle_4_deg22.247
r_dihedral_angle_3_deg17.756
r_lrange_it12.015
r_scangle_it9.853
r_scbond_it7.1
r_mcangle_it6.524
r_dihedral_angle_1_deg5.125
r_mcbond_it4.701
r_angle_refined_deg1.605
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.746
r_dihedral_angle_4_deg22.247
r_dihedral_angle_3_deg17.756
r_lrange_it12.015
r_scangle_it9.853
r_scbond_it7.1
r_mcangle_it6.524
r_dihedral_angle_1_deg5.125
r_mcbond_it4.701
r_angle_refined_deg1.605
r_nbtor_refined0.311
r_symmetry_nbd_refined0.259
r_nbd_refined0.206
r_symmetry_xyhbond_nbd_refined0.143
r_xyhbond_nbd_refined0.109
r_chiral_restr0.105
r_ncsr_local_group_30.105
r_ncsr_local_group_60.097
r_ncsr_local_group_50.092
r_ncsr_local_group_40.09
r_ncsr_local_group_20.088
r_ncsr_local_group_10.085
r_bond_refined_d0.008
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9005
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing