3JQF

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 1,3,5-triazine-2,4,6-triamine (AX2)


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
2.0439.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.549α = 90
b = 90.241β = 115.57
c = 82.407γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Vertically focusing mirror, Rh coated, water cooled2006-09-17SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.11.48800SRSPX14.1

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
11.623.3892.50.0340.03412.43119467
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)
11.61.69880.3470.3472.13.216541

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 2C7V1.623.38119437599992.180.1470.1450.186RANDOM21.438
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]
-1.35-0.761.94-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.939
r_dihedral_angle_4_deg18.725
r_dihedral_angle_3_deg13.237
r_dihedral_angle_1_deg5.739
r_scangle_it5.442
r_scbond_it3.975
r_mcangle_it2.735
r_mcbond_it2.041
r_angle_refined_deg1.601
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.939
r_dihedral_angle_4_deg18.725
r_dihedral_angle_3_deg13.237
r_dihedral_angle_1_deg5.739
r_scangle_it5.442
r_scbond_it3.975
r_mcangle_it2.735
r_mcbond_it2.041
r_angle_refined_deg1.601
r_nbtor_refined0.301
r_symmetry_vdw_refined0.24
r_nbd_refined0.209
r_symmetry_hbond_refined0.199
r_xyhbond_nbd_refined0.187
r_chiral_restr0.099
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7405
Nucleic Acid Atoms
Solvent Atoms1059
Heterogen Atoms336

Software

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