3JQB

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-5-(2-phenylethyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one (DX6)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C7VPDB entry 2C7V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2932-3M Sodium acetate, 10-100mM Sodium citrate, pH 4.0-6.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0540

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.671α = 90
b = 90.433β = 115.54
c = 82.564γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDPt coated mirrors in a Kirkpatrick-Baez (KB) geometry2006-05-20SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87300ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.445.2298.70.110.119.42.638283
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.5399.20.1290.1294.22.65561

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 REPLACEMENTTHROUGHOUTPDB entry 2C7V2.445.2238265195298.520.1950.1920.252RANDOM7.994
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]
-1.40.221.66-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.698
r_dihedral_angle_4_deg14.059
r_dihedral_angle_3_deg14.045
r_dihedral_angle_1_deg4.934
r_scangle_it2.508
r_scbond_it1.739
r_mcangle_it1.335
r_angle_refined_deg1.004
r_mcbond_it0.796
r_nbtor_refined0.289
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.698
r_dihedral_angle_4_deg14.059
r_dihedral_angle_3_deg14.045
r_dihedral_angle_1_deg4.934
r_scangle_it2.508
r_scbond_it1.739
r_mcangle_it1.335
r_angle_refined_deg1.004
r_mcbond_it0.796
r_nbtor_refined0.289
r_nbd_refined0.168
r_symmetry_vdw_refined0.134
r_xyhbond_nbd_refined0.111
r_symmetry_hbond_refined0.105
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7427
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms257

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing