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Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (Compound AX3)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 2-3M sodium acetate, 10-100mM sodium citrate, pH 4.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.84 α = 90 b = 87.5 β = 116.08 c = 84.23 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 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.98 75.59 95.8 0.073 14.12 64386 -3 26.881
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 1.98 2.04 91.5 0.343 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.98 75.59 64384 3209 96 0.209 0.206 0.2134 0.267 0.2684 RANDOM 24.048
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] -2.63 -1.84 3.73 -2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 22.869 r_dihedral_angle_3_deg 19.078 r_dihedral_angle_1_deg 6.195 r_scangle_it 4.783 r_scbond_it 3.661 r_angle_refined_deg 2.028 r_mcangle_it 1.919 r_mcbond_it 1.54 r_angle_other_deg 1.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 22.869 r_dihedral_angle_3_deg 19.078 r_dihedral_angle_1_deg 6.195 r_scangle_it 4.783 r_scbond_it 3.661 r_angle_refined_deg 2.028 r_mcangle_it 1.919 r_mcbond_it 1.54 r_angle_other_deg 1.043 r_symmetry_hbond_refined 0.25 r_mcbond_other 0.234 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.216 r_symmetry_vdw_other 0.216 r_nbd_other 0.193 r_nbtor_refined 0.188 r_chiral_restr 0.107 r_nbtor_other 0.092 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7501 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 292
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction