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Trypanosoma brucei PTR1 in complex with inhibitor NP-29
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein solution: 8 g/L in 20 mM Tris-HCl pH 7.5, 10 mM DTT; crystallization buffer: 0.1 M sodium citrate pH 5, 2.25 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 1.93 36.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.68 α = 90 b = 89.73 β = 115.71 c = 82.84 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 PILATUS 6M-F 2014-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.43 41.77 94.5 0.044 9.2 2.2 171130 2 12.8
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 1.43 1.51 94.2 0.357 2 2.1
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 2X9G 1.43 37.33 162483 8611 94.4 0.14604 0.14423 0.1441 0.17953 0.1793 RANDOM 21.037
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] 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.119 r_sphericity_free 32.988 r_dihedral_angle_4_deg 17.295 r_sphericity_bonded 12.677 r_dihedral_angle_3_deg 12.012 r_dihedral_angle_1_deg 5.464 r_long_range_B_refined 3.631 r_mcangle_it 2.665 r_scbond_it 2.444 r_rigid_bond_restr 2.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.119 r_sphericity_free 32.988 r_dihedral_angle_4_deg 17.295 r_sphericity_bonded 12.677 r_dihedral_angle_3_deg 12.012 r_dihedral_angle_1_deg 5.464 r_long_range_B_refined 3.631 r_mcangle_it 2.665 r_scbond_it 2.444 r_rigid_bond_restr 2.363 r_mcbond_it 2.194 r_angle_refined_deg 1.418 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7214 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms 233
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing