3WXJ

Crystal structure of trypanosoma brucei gambiense glycerol kinase in complex with glycerol 3-phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320-30% PEG 400, 0.1M HEPES, 0.01M MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6152.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.165α = 90
b = 120.89β = 90.02
c = 153.553γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

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
12.75099.80.04617.63.76445361192-3
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)
12.72.7599.80.4513.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.7506445361192319699.470.210.209850.205740.29022RANDOM66.603
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]
-20.845.9654.23-33.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.399
r_dihedral_angle_3_deg20.802
r_dihedral_angle_4_deg18.687
r_dihedral_angle_1_deg6.544
r_scangle_it1.39
r_angle_refined_deg1.24
r_scbond_it0.845
r_mcangle_it0.756
r_mcbond_it0.412
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.399
r_dihedral_angle_3_deg20.802
r_dihedral_angle_4_deg18.687
r_dihedral_angle_1_deg6.544
r_scangle_it1.39
r_angle_refined_deg1.24
r_scbond_it0.845
r_mcangle_it0.756
r_mcbond_it0.412
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15828
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms36

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling