8Y1T | pdb_00008y1t

CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI GAMBIENSE GLYCEROL KINASE COMPLEX WITH ADP and G3P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6J9V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52938-18% PEG 400, 0.1M HEPES, 11% 1,6-HEXANEDIOL, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.652.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.563α = 90
b = 121.741β = 90
c = 154.278γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.45099.80.0540.99918.513.645369
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5599.10.7190.842212.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6J9V2.419.8644323232699.750.195180.192260.20750.249820.257RANDOM73.455
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]
0.07-0.04-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.494
r_dihedral_angle_3_deg18.103
r_dihedral_angle_4_deg18.091
r_long_range_B_refined9.947
r_long_range_B_other9.947
r_scangle_other7.626
r_dihedral_angle_1_deg7.021
r_mcangle_it6.29
r_mcangle_other6.289
r_scbond_it5.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.494
r_dihedral_angle_3_deg18.103
r_dihedral_angle_4_deg18.091
r_long_range_B_refined9.947
r_long_range_B_other9.947
r_scangle_other7.626
r_dihedral_angle_1_deg7.021
r_mcangle_it6.29
r_mcangle_other6.289
r_scbond_it5.129
r_scbond_other5.129
r_mcbond_it4.515
r_mcbond_other4.515
r_angle_refined_deg1.565
r_angle_other_deg1.002
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7912
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing