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Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6-phenylpteridine-2,4,7-triamine (DX2)
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 2.03 39.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.538 α = 90 b = 90.029 β = 115.49 c = 82.359 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 2006-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.00640 ESRF ID23-1
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 1.8 74.34 99.7 0.036 0.036 11.6 2.8 90613
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 1.9 100 0.25 0.25 3 2.9 13225
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 1.8 74.33 90587 4569 99.62 0.154 0.152 0.154 0.191 0.1923 RANDOM 28.332
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] -1.97 -0.79 2.31 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.995 r_dihedral_angle_4_deg 17.741 r_dihedral_angle_3_deg 14.115 r_scangle_it 6.029 r_dihedral_angle_1_deg 5.566 r_scbond_it 4.693 r_mcangle_it 3.258 r_mcbond_it 2.374 r_angle_refined_deg 1.501 r_symmetry_hbond_refined 0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.995 r_dihedral_angle_4_deg 17.741 r_dihedral_angle_3_deg 14.115 r_scangle_it 6.029 r_dihedral_angle_1_deg 5.566 r_scbond_it 4.693 r_mcangle_it 3.258 r_mcbond_it 2.374 r_angle_refined_deg 1.501 r_symmetry_hbond_refined 0.358 r_nbtor_refined 0.304 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7338 Nucleic Acid Atoms Solvent Atoms 611 Heterogen Atoms 284
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing