3JQC

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-6-bromo-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (JU2)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION52932-3M Sodium acetate, 10-100mM Sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0339.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.862α = 90
b = 89.114β = 116.08
c = 84.246γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-09-20SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM160.97897ESRFBM16

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
11.827.6592.90.0470.04711.9384262
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)
11.81.965.20.3770.37722.78604

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 2C7V1.827.6584237426292.790.170.1680.204RANDOM18.318
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]
-2.12-1.052.55-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.71
r_dihedral_angle_4_deg17.915
r_dihedral_angle_3_deg14.915
r_dihedral_angle_1_deg5.583
r_scangle_it5.387
r_scbond_it4.272
r_mcangle_it2.514
r_mcbond_it1.751
r_angle_refined_deg1.424
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.71
r_dihedral_angle_4_deg17.915
r_dihedral_angle_3_deg14.915
r_dihedral_angle_1_deg5.583
r_scangle_it5.387
r_scbond_it4.272
r_mcangle_it2.514
r_mcbond_it1.751
r_angle_refined_deg1.424
r_nbtor_refined0.295
r_symmetry_vdw_refined0.211
r_nbd_refined0.193
r_symmetry_hbond_refined0.181
r_xyhbond_nbd_refined0.138
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7428
Nucleic Acid Atoms
Solvent Atoms731
Heterogen Atoms248

Software

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