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Drosophila PGRP-LB Y78F mutant
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 7 293 0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.69 27.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.502 α = 90 b = 40.502 β = 90 c = 338.941 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER2 XE 16M 2019-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
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 1.3 338.94 99.9 0.096 0.098 0.022 0.998 20.8 31.5 42802
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 1.3 1.32 0.443 0.478 0.176 0.955 13
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 1.3 56.554 42582 2133 99.939 0.188 0.1864 0.1922 0.2207 0.2249 13.906
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] 0.147 0.073 0.147 -0.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.19 r_dihedral_angle_4_deg 15.455 r_dihedral_angle_3_deg 10.466 r_dihedral_angle_1_deg 7.009 r_lrange_it 4.116 r_lrange_other 4.115 r_scangle_it 3.098 r_scangle_other 3.096 r_scbond_it 2.099 r_scbond_other 2.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.19 r_dihedral_angle_4_deg 15.455 r_dihedral_angle_3_deg 10.466 r_dihedral_angle_1_deg 7.009 r_lrange_it 4.116 r_lrange_other 4.115 r_scangle_it 3.098 r_scangle_other 3.096 r_scbond_it 2.099 r_scbond_other 2.099 r_angle_refined_deg 1.904 r_mcangle_it 1.868 r_mcangle_other 1.861 r_angle_other_deg 1.524 r_mcbond_it 1.288 r_mcbond_other 1.277 r_nbd_other 0.26 r_symmetry_nbd_refined 0.231 r_nbd_refined 0.22 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.131 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.085 r_symmetry_metal_ion_refined 0.063 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1337 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 17
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