3JQ6

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6,7-bis(1-methylethyl)pteridine-2,4-diamine (DX1)


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
2.0640.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.141α = 90
b = 89.468β = 115.48
c = 84.342γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rLiquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror2005-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97550ESRFID29

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
11.830.6699.90.080.0813.54.392014
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)
11.81.91000.3640.3641.94.313424

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 2C7V1.830.6691988465099.910.1520.150.19RANDOM17.935
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]
-1.52-0.512.99-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.104
r_dihedral_angle_4_deg19.346
r_dihedral_angle_3_deg14.184
r_dihedral_angle_1_deg5.597
r_scangle_it4.93
r_scbond_it3.719
r_mcangle_it2.516
r_mcbond_it1.791
r_angle_refined_deg1.305
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.104
r_dihedral_angle_4_deg19.346
r_dihedral_angle_3_deg14.184
r_dihedral_angle_1_deg5.597
r_scangle_it4.93
r_scbond_it3.719
r_mcangle_it2.516
r_mcbond_it1.791
r_angle_refined_deg1.305
r_nbtor_refined0.301
r_symmetry_vdw_refined0.23
r_nbd_refined0.198
r_xyhbond_nbd_refined0.186
r_symmetry_hbond_refined0.183
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7397
Nucleic Acid Atoms
Solvent Atoms1023
Heterogen Atoms296

Software

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