7S2P

Crystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in complex with inhibitor CBZ-GlcN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q2R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295A ligand-free TcGlcK(F337L) crystal was soaked in 1.0 mM CBZ-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 15% (w/v) PEG 3,350 for 24 hours
Crystal Properties
Matthews coefficientSolvent content
2.4549.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.227α = 90
b = 78.951β = 94.86
c = 77.027γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B0.9792APS14-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
12.354099.10.0520.02735.33.733656-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.3998.20.7180.3720.70223.6

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 REPLACEMENTTHROUGHOUT2Q2R2.3538.431970167998.690.20410.20150.255RANDOM71.278
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]
-2.671.312.150.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.739
r_dihedral_angle_4_deg18.318
r_dihedral_angle_3_deg13.979
r_dihedral_angle_1_deg7.257
r_angle_other_deg2.353
r_angle_refined_deg1.67
r_chiral_restr0.077
r_bond_other_d0.035
r_gen_planes_other0.013
r_bond_refined_d0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.739
r_dihedral_angle_4_deg18.318
r_dihedral_angle_3_deg13.979
r_dihedral_angle_1_deg7.257
r_angle_other_deg2.353
r_angle_refined_deg1.67
r_chiral_restr0.077
r_bond_other_d0.035
r_gen_planes_other0.013
r_bond_refined_d0.012
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5627
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing