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Drosophila PGRP-LB Y78F mutant in complex with tracheal cytotoxin (TCT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 30% v/v 2-Propanol, 100 mM Tris base HCl pH 8.5, 30% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.587 α = 92.113 b = 52.167 β = 105.123 c = 55.579 γ = 111.513
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 2019-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.969 Diamond I24
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 1.8 53.07 97.7 0.084 0.098 0.05 0.998 11.9 6.9 34852
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 1.8 1.84 0.478 0.56 0.289 0.891 6.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1OHT 1.8 53.067 34851 1760 97.742 0.146 0.1447 0.157 0.1798 0.1908 19.093
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] 0.659 0.031 -0.431 0.125 -0.47 -0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.466 r_dihedral_angle_3_deg 11.766 r_dihedral_angle_4_deg 11.686 r_dihedral_angle_1_deg 7.175 r_lrange_it 5.587 r_lrange_other 5.555 r_scangle_it 4.383 r_scangle_other 4.382 r_scbond_it 2.907 r_scbond_other 2.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.466 r_dihedral_angle_3_deg 11.766 r_dihedral_angle_4_deg 11.686 r_dihedral_angle_1_deg 7.175 r_lrange_it 5.587 r_lrange_other 5.555 r_scangle_it 4.383 r_scangle_other 4.382 r_scbond_it 2.907 r_scbond_other 2.906 r_mcangle_it 2.567 r_mcangle_other 2.566 r_mcbond_it 1.911 r_mcbond_other 1.911 r_angle_refined_deg 1.684 r_angle_other_deg 1.479 r_symmetry_nbd_refined 0.333 r_nbd_refined 0.213 r_nbd_other 0.179 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_other 0.061 r_ncsr_local_group_1 0.051 r_metal_ion_refined 0.043 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2625 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data reduction DIALS data processing Coot model building GDA data collection Aimless data scaling PHASER phasing