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LppS with covalent adduct derived from 1c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.25 293 Well solution: 0.1 M Na-Citrate pH 4.25 / 17.5% PEG 6K
The ligand was added to the soaking solution at 4 mM concentration.
In the soaking drop,
Citrate is replaced by Acetate (0.3 M)
150 mM NaCl
0.1 M Bis-Tris pH 6.2
0.3 M Na-Acetate pH 5.2
25% PEG 6K
PEG 6K INCREASED to 25% FOR CRYO-PROTECTION
Crystal Properties Matthews coefficient Solvent content 2.1 41.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.309 α = 90 b = 74.873 β = 111.52 c = 67.764 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 EIGER X 16M mirrors (VFM, HFM) 2019-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.82656 MAX IV BioMAX
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 1.77 25.15 99.7 0.088 10.1 6.9 45504 2.1 17.8
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 1.77 1.81 94.5 0.658 2.1 6.3
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 5LBG 1.77 25 43132 2236 99.4 0.167 0.165 0.173 0.214 0.2221 RANDOM 29.57
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] -2.2 0.85 -0.26 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.064 r_dihedral_angle_4_deg 14.585 r_dihedral_angle_3_deg 12.639 r_dihedral_angle_1_deg 5.96 r_angle_refined_deg 1.699 r_angle_other_deg 1.036 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.064 r_dihedral_angle_4_deg 14.585 r_dihedral_angle_3_deg 12.639 r_dihedral_angle_1_deg 5.96 r_angle_refined_deg 1.699 r_angle_other_deg 1.036 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3982 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing