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Trypanosoma brucei PTR1 (TbPTR1) in complex with pyrimethamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 294 2-2.5M sodium acetate, 0.1M sodium citrate, pH 5
Crystal Properties Matthews coefficient Solvent content 2.1 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.9 α = 90 b = 91.03 β = 115.63 c = 82.8 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 PIXEL DECTRIS PILATUS3 6M 2015-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9184 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.34 18.28 93.9 0.056 0.071 0.042 0.998 7.6 2.3 210248 11.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.41 94.2 0.345 0.44 0.27 0.883 2.3 2.2
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 6TBX 1.34 18.07 199465 10516 93.76 0.1323 0.1301 0.1313 0.1739 0.1744 RANDOM 18.906
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] -0.02 0.08 -0.45 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.731 r_dihedral_angle_4_deg 19.903 r_dihedral_angle_3_deg 12.715 r_dihedral_angle_1_deg 6.218 r_rigid_bond_restr 5.042 r_angle_refined_deg 2.076 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7289 Nucleic Acid Atoms Solvent Atoms 1025 Heterogen Atoms 282
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing