5XQA

Crystal Structure of Transketolase in complex with ribose-5-phosphate from Pichia Stipitis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HYV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1M MES, 0.1M NaCl, PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.0860.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.093α = 90
b = 184.78β = 90
c = 99.015γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

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
11.143096.60.05116.94.6305278
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.141.18962.23.7

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 REPLACEMENTTHROUGHOUT5HYV1.14303052781602596.490.130070.129490.14121RANDOM9.189
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]
-0.150.3-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.812
r_sphericity_free26.793
r_dihedral_angle_4_deg15.151
r_dihedral_angle_3_deg11.241
r_dihedral_angle_1_deg5.968
r_sphericity_bonded5.679
r_rigid_bond_restr4.209
r_long_range_B_refined2.786
r_long_range_B_other2.786
r_angle_refined_deg1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.812
r_sphericity_free26.793
r_dihedral_angle_4_deg15.151
r_dihedral_angle_3_deg11.241
r_dihedral_angle_1_deg5.968
r_sphericity_bonded5.679
r_rigid_bond_restr4.209
r_long_range_B_refined2.786
r_long_range_B_other2.786
r_angle_refined_deg1.45
r_scangle_other1.032
r_angle_other_deg0.999
r_scbond_other0.916
r_scbond_it0.915
r_mcangle_other0.731
r_mcangle_it0.73
r_mcbond_it0.518
r_mcbond_other0.517
r_chiral_restr0.083
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5130
Nucleic Acid Atoms
Solvent Atoms1027
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling