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Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6,7,7-trimethyl-7,8-dihydropteridine-2,4-diamine (DX3)
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 2.05 39.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.097 α = 90 b = 89.154 β = 115.49 c = 84.187 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 315r Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror 2005-12-14 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97550 ESRF ID29
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 1.95 66.89 98.5 0.066 0.066 10.4 4.3 70867
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 1.95 2.06 97.6 0.22 0.22 3.2 4.8 10236
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 1.95 66.89 70417 3569 97.71 0.232 0.229 0.2261 0.281 0.2742 RANDOM 15.454
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] -0.22 0.55 1 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.898 r_dihedral_angle_4_deg 15.9 r_dihedral_angle_3_deg 14.604 r_dihedral_angle_1_deg 5.249 r_angle_refined_deg 1.101 r_scangle_it 1.023 r_scbond_it 0.652 r_mcangle_it 0.549 r_mcbond_it 0.313 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.898 r_dihedral_angle_4_deg 15.9 r_dihedral_angle_3_deg 14.604 r_dihedral_angle_1_deg 5.249 r_angle_refined_deg 1.101 r_scangle_it 1.023 r_scbond_it 0.652 r_mcangle_it 0.549 r_mcbond_it 0.313 r_nbtor_refined 0.293 r_nbd_refined 0.178 r_symmetry_vdw_refined 0.137 r_xyhbond_nbd_refined 0.124 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7363 Nucleic Acid Atoms Solvent Atoms 976 Heterogen Atoms 260
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection