3JQD

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-4-oxo-6-phenyl-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (DX7)


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
2.1141.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.641α = 90
b = 90.731β = 115.33
c = 84.636γ = 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) geometry2005-05-20MSINGLE 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
11.638.9881.70.0890.08910.23.1108123
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)
11.61.6984.90.3320.3322.22.916413

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 2C7V1.638.4108063543480.70.1810.1790.216RANDOM16.228
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]
-0.73-0.31.58-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.552
r_dihedral_angle_4_deg14.589
r_dihedral_angle_3_deg12.036
r_dihedral_angle_1_deg5.261
r_scangle_it3.357
r_scbond_it2.544
r_mcangle_it1.697
r_mcbond_it1.406
r_angle_refined_deg1.154
r_angle_other_deg0.846
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.552
r_dihedral_angle_4_deg14.589
r_dihedral_angle_3_deg12.036
r_dihedral_angle_1_deg5.261
r_scangle_it3.357
r_scbond_it2.544
r_mcangle_it1.697
r_mcbond_it1.406
r_angle_refined_deg1.154
r_angle_other_deg0.846
r_mcbond_other0.383
r_nbd_refined0.191
r_symmetry_vdw_other0.184
r_nbd_other0.174
r_nbtor_refined0.166
r_symmetry_vdw_refined0.131
r_symmetry_hbond_refined0.128
r_xyhbond_nbd_refined0.105
r_nbtor_other0.081
r_chiral_restr0.057
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7404
Nucleic Acid Atoms
Solvent Atoms1196
Heterogen Atoms272

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOLREPphasing