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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)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C7V PDB entry 2C7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 2-3M Sodium acetate, 10-100mM Sodium citrate, pH 4.0-6.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.641 α = 90 b = 90.731 β = 115.33 c = 84.636 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry 2005-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87300 ESRF ID23-2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 38.98 81.7 0.089 0.089 10.2 3.1 108123
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) Redundancy Number Unique Reflections (All) 1 1.6 1.69 84.9 0.332 0.332 2.2 2.9 16413
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2C7V 1.6 38.4 108063 5434 80.7 0.181 0.179 0.186 0.216 0.2206 RANDOM 16.228
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 -0.3 1.58 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.552 r_dihedral_angle_4_deg 14.589 r_dihedral_angle_3_deg 12.036 r_dihedral_angle_1_deg 5.261 r_scangle_it 3.357 r_scbond_it 2.544 r_mcangle_it 1.697 r_mcbond_it 1.406 r_angle_refined_deg 1.154 r_angle_other_deg 0.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.552 r_dihedral_angle_4_deg 14.589 r_dihedral_angle_3_deg 12.036 r_dihedral_angle_1_deg 5.261 r_scangle_it 3.357 r_scbond_it 2.544 r_mcangle_it 1.697 r_mcbond_it 1.406 r_angle_refined_deg 1.154 r_angle_other_deg 0.846 r_mcbond_other 0.383 r_nbd_refined 0.191 r_symmetry_vdw_other 0.184 r_nbd_other 0.174 r_nbtor_refined 0.166 r_symmetry_vdw_refined 0.131 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_refined 0.105 r_nbtor_other 0.081 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7404 Nucleic Acid Atoms Solvent Atoms 1196 Heterogen Atoms 272
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOLREP phasing