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High resolution crystal structure of N-terminal domain of PEX14 from Trypanosoma brucei in complex with the fist compound with sub-micromolar trypanocidal activity
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2M MgCl2, 0.1 M Tris pH 8, 20% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.46 50.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.935 α = 90 b = 45.935 β = 90 c = 63.733 γ = 120
Symmetry Space Group P 32 2 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 2017-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.2 39.78 93.7 0.072 0.082 0.996 9.42 3.93 23334 15.045
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.3 86.3 0.291 0.345 0.89 2.97 3.367
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 1.2 39.78 22179 1155 93.7 0.1106 0.1084 0.1079 0.1524 0.1516 RANDOM 13.924
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 -0.01 -0.03 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_sphericity_free 28.747 r_dihedral_angle_3_deg 15.104 r_sphericity_bonded 12.171 r_dihedral_angle_4_deg 10.064 r_rigid_bond_restr 6.465 r_dihedral_angle_1_deg 4.628 r_angle_refined_deg 2.67 r_angle_other_deg 1.289 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.458 r_sphericity_free 28.747 r_dihedral_angle_3_deg 15.104 r_sphericity_bonded 12.171 r_dihedral_angle_4_deg 10.064 r_rigid_bond_restr 6.465 r_dihedral_angle_1_deg 4.628 r_angle_refined_deg 2.67 r_angle_other_deg 1.289 r_chiral_restr 0.134 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 552 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 68
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction