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Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small molecules designed to investigate the water envelope
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AON
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2M Na2SO4, 0.1 M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.78 α = 90 b = 115.52 β = 101.39 c = 38.87 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 2017-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1 PETRA III, DESY P11
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 1.3 20 96.8 0.028 0.035 0.999 14.55 2.512 145521 -3 23.445
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 1.3 1.35 98.4 0.468 0.577 0.824 1.81 2.406
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 5AON 1.3 20 71864 3575 99.62 0.1627 0.1614 0.1647 0.1889 0.1579 RANDOM 21.234
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] -0.37 -0.71 1.06 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.819 r_dihedral_angle_4_deg 19.632 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_1_deg 4.977 r_angle_refined_deg 3.125 r_angle_other_deg 3.118 r_chiral_restr 0.18 r_bond_refined_d 0.037 r_bond_other_d 0.022 r_gen_planes_refined 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.819 r_dihedral_angle_4_deg 19.632 r_dihedral_angle_3_deg 14.127 r_dihedral_angle_1_deg 4.977 r_angle_refined_deg 3.125 r_angle_other_deg 3.118 r_chiral_restr 0.18 r_bond_refined_d 0.037 r_bond_other_d 0.022 r_gen_planes_refined 0.018 r_gen_planes_other 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2076 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 202
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing