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Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-6-bromo-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (JU2)
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 5 293 2-3M Sodium acetate, 10-100mM Sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.862 α = 90 b = 89.114 β = 116.08 c = 84.246 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 ADSC QUANTUM 210 2006-09-20 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.97897 ESRF BM16
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 1.8 27.65 92.9 0.047 0.047 11.9 3 84262
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 1.8 1.9 65.2 0.377 0.377 2 2.7 8604
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2C7V 1.8 27.65 84237 4262 92.79 0.17 0.168 0.204 0.201 RANDOM 18.318
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] -2.12 -1.05 2.55 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.71 r_dihedral_angle_4_deg 17.915 r_dihedral_angle_3_deg 14.915 r_dihedral_angle_1_deg 5.583 r_scangle_it 5.387 r_scbond_it 4.272 r_mcangle_it 2.514 r_mcbond_it 1.751 r_angle_refined_deg 1.424 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.71 r_dihedral_angle_4_deg 17.915 r_dihedral_angle_3_deg 14.915 r_dihedral_angle_1_deg 5.583 r_scangle_it 5.387 r_scbond_it 4.272 r_mcangle_it 2.514 r_mcbond_it 1.751 r_angle_refined_deg 1.424 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7428 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 248
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection