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Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6-[(4-methoxybenzyl)sulfanyl]pyrimidine-2,4-diamine (AX6)
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 39.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.531 α = 90 b = 89.845 β = 115.53 c = 82.437 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 225 mm CCD Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry 2006-05-20 M 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) 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 53.2 96.5 0.092 2.4 74417
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.01 0.29 1.9 2.7
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 1.9 53.2 74400 3738 96.27 0.214 0.211 0.2109 0.267 0.2631 RANDOM 17.855
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] -2.9 -1.19 3.07 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.048 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 14.812 r_dihedral_angle_1_deg 5.9 r_scangle_it 4.533 r_scbond_it 3.687 r_mcangle_it 2.497 r_mcbond_it 1.681 r_angle_refined_deg 1.531 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.048 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 14.812 r_dihedral_angle_1_deg 5.9 r_scangle_it 4.533 r_scbond_it 3.687 r_mcangle_it 2.497 r_mcbond_it 1.681 r_angle_refined_deg 1.531 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.201 r_symmetry_hbond_refined 0.181 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7406 Nucleic Acid Atoms Solvent Atoms 612 Heterogen Atoms 264
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection