5XRY

Crystal Structure of Transketolase contains cysteinesufonic acid 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
3.0960.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.267α = 90
b = 185.551β = 90
c = 98.878γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2017-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A10.9900NSRRCBL15A1

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
11.33099.90.0528.48.1224909

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 REPLACEMENTTHROUGHOUT5HYV1.3302014791044993.90.137370.136520.15368RANDOM16.034
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]
-0.110.17-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.926
r_sphericity_free21.112
r_dihedral_angle_4_deg16.113
r_dihedral_angle_3_deg12.298
r_dihedral_angle_1_deg5.926
r_sphericity_bonded5.491
r_rigid_bond_restr3.15
r_long_range_B_other2.228
r_long_range_B_refined2.227
r_scangle_other1.702
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.926
r_sphericity_free21.112
r_dihedral_angle_4_deg16.113
r_dihedral_angle_3_deg12.298
r_dihedral_angle_1_deg5.926
r_sphericity_bonded5.491
r_rigid_bond_restr3.15
r_long_range_B_other2.228
r_long_range_B_refined2.227
r_scangle_other1.702
r_scbond_it1.515
r_scbond_other1.514
r_angle_refined_deg1.455
r_mcangle_it1.283
r_mcangle_other1.283
r_mcbond_it1.018
r_mcbond_other1.017
r_angle_other_deg0.989
r_chiral_restr0.091
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms5133
Nucleic Acid Atoms
Solvent Atoms499
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling