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Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-1,9-dihydro-6H-purine-6-thione (DX4)
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 2.07 40.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.997 α = 90 b = 90.834 β = 115.5 c = 82.64 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 2006-05-21 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 1.9 57.64 99.9 0.057 0.057 9.9 3 78741
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 1.9 2 99.9 0.32 0.32 2.1 3.3 11433
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 1.9 57.64 78702 3960 99.87 0.149 0.147 0.189 0.2317 RANDOM 23.802
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] -1.22 -0.54 1.63 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.73 r_dihedral_angle_4_deg 16.781 r_dihedral_angle_3_deg 13.448 r_dihedral_angle_1_deg 5.566 r_scangle_it 5.252 r_scbond_it 4.05 r_mcangle_it 2.828 r_mcbond_it 2.418 r_angle_refined_deg 1.342 r_angle_other_deg 0.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.73 r_dihedral_angle_4_deg 16.781 r_dihedral_angle_3_deg 13.448 r_dihedral_angle_1_deg 5.566 r_scangle_it 5.252 r_scbond_it 4.05 r_mcangle_it 2.828 r_mcbond_it 2.418 r_angle_refined_deg 1.342 r_angle_other_deg 0.937 r_mcbond_other 0.638 r_symmetry_hbond_refined 0.239 r_symmetry_vdw_other 0.232 r_nbd_refined 0.196 r_nbd_other 0.182 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.124 r_nbtor_other 0.084 r_chiral_restr 0.073 r_xyhbond_nbd_other 0.021 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7414 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 236
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOLREP phasing