4KXY

Human transketolase in complex with ThDP analogue (R)-2-(1,2-dihydroxyethyl)-3-deaza-ThDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MOSPDB ENTRY 3MOS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.9293Reservoir mixture of 13.5-15 % PEG 6000 (W/V), 4% PEG 400 (v/v), 2 % glycerol (v/v), pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.15α = 90
b = 86.05β = 94.12
c = 92.73γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2011-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9841BESSY14.1

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
11.263099.60.06613.073.1307778307778-314.88
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)
11.261.3699.70.5992.25

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONFOURIER SYNTHESISFREE RPDB ENTRY 3MOS1.26303077783077781742499.70.16510.15380.15380.2038RANDOM16.4439
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
s_angle_d318
s_similar_dist67
s_zero_chiral_vol51
s_non_zero_chiral_vol4
s_approx_iso_adps0.159
s_anti_bump_dis_restr0.058
s_bond_d0.012
s_rigid_bond_adp_cmpnt0.011
s_from_restr_planes
s_similar_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9494
Nucleic Acid Atoms
Solvent Atoms1462
Heterogen Atoms182

Software

Software
Software NamePurpose
XSCALEdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction
PHENIXphasing
SHELXLrefinement