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Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and substrate (folate)
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 1.98 37.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.441 α = 90 b = 88.596 β = 115.34 c = 81.587 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 IMAGE PLATE RIGAKU RAXIS IV mirrors SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.6 73.737 81.1 0.068 0.068 9.1 2.2 23556
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 2.6 2.74 74 0.377 0.377 2 2.3 3152
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 2.6 37.67 23539 1224 79.49 0.192 0.189 0.1895 0.244 0.2375 RANDOM 30.712
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] -4.56 -2.83 7.48 -5.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.998 r_dihedral_angle_4_deg 18.618 r_dihedral_angle_3_deg 17.034 r_dihedral_angle_1_deg 5.444 r_angle_refined_deg 1.46 r_scangle_it 1.239 r_scbond_it 0.92 r_mcangle_it 0.548 r_symmetry_hbond_refined 0.418 r_symmetry_vdw_refined 0.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.998 r_dihedral_angle_4_deg 18.618 r_dihedral_angle_3_deg 17.034 r_dihedral_angle_1_deg 5.444 r_angle_refined_deg 1.46 r_scangle_it 1.239 r_scbond_it 0.92 r_mcangle_it 0.548 r_symmetry_hbond_refined 0.418 r_symmetry_vdw_refined 0.366 r_mcbond_it 0.331 r_nbtor_refined 0.303 r_xyhbond_nbd_refined 0.286 r_nbd_refined 0.207 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7405 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 320
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection