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Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 1,3,5-triazine-2,4,6-triamine (AX2)
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 2.04 39.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.549 α = 90 b = 90.241 β = 115.57 c = 82.407 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 4 Vertically focusing mirror, Rh coated, water cooled 2006-09-17 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.48800 SRS PX14.1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 23.38 92.5 0.034 0.034 12.4 3 119467
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 88 0.347 0.347 2.1 3.2 16541
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 23.38 119437 5999 92.18 0.147 0.145 0.1435 0.186 0.1847 RANDOM 21.438
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] -1.35 -0.76 1.94 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.939 r_dihedral_angle_4_deg 18.725 r_dihedral_angle_3_deg 13.237 r_dihedral_angle_1_deg 5.739 r_scangle_it 5.442 r_scbond_it 3.975 r_mcangle_it 2.735 r_mcbond_it 2.041 r_angle_refined_deg 1.601 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.939 r_dihedral_angle_4_deg 18.725 r_dihedral_angle_3_deg 13.237 r_dihedral_angle_1_deg 5.739 r_scangle_it 5.442 r_scbond_it 3.975 r_mcangle_it 2.735 r_mcbond_it 2.041 r_angle_refined_deg 1.601 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.199 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.099 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7405 Nucleic Acid Atoms Solvent Atoms 1059 Heterogen Atoms 336
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection