3JQ7

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6-phenylpteridine-2,4,7-triamine (DX2)


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
2.0339.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.538α = 90
b = 90.029β = 115.49
c = 82.359γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2006-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.00640ESRFID23-1

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
11.874.3499.70.0360.03611.62.890613
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)
11.81.91000.250.2532.913225

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 2C7V1.874.3390587456999.620.1540.1520.191RANDOM28.332
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]
-1.97-0.792.31-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.995
r_dihedral_angle_4_deg17.741
r_dihedral_angle_3_deg14.115
r_scangle_it6.029
r_dihedral_angle_1_deg5.566
r_scbond_it4.693
r_mcangle_it3.258
r_mcbond_it2.374
r_angle_refined_deg1.501
r_symmetry_hbond_refined0.358
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.995
r_dihedral_angle_4_deg17.741
r_dihedral_angle_3_deg14.115
r_scangle_it6.029
r_dihedral_angle_1_deg5.566
r_scbond_it4.693
r_mcangle_it3.258
r_mcbond_it2.374
r_angle_refined_deg1.501
r_symmetry_hbond_refined0.358
r_nbtor_refined0.304
r_nbd_refined0.208
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.177
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7338
Nucleic Acid Atoms
Solvent Atoms611
Heterogen Atoms284

Software

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