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Crystal structure of Schistosoma mansoni HDAC8 in complex with a 3-chlorophenyl-spiroindoline capped hydroxamate-based inhibitor, bound to a novel site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 20-22% PEG 3350, 200mM sodium/potassium tartrate
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.369 α = 90 b = 70.369 β = 90 c = 186.346 γ = 90
Symmetry Space Group P 41 21 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 PILATUS 6M 2020-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
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 46.63 100 0.091 0.095 0.027 0.999 15 12.6 44460
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 99.3 3.534 3.693 1.06 0.498 11.9
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 4bz5 1.8 46.63 42160 2204 99.94 0.1808 0.179 0.1886 0.2132 0.2153 RANDOM 40.964
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] 1.35 1.35 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_dihedral_angle_4_deg 21.49 r_dihedral_angle_3_deg 14.836 r_dihedral_angle_1_deg 5.934 r_angle_refined_deg 1.56 r_angle_other_deg 1.358 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_dihedral_angle_4_deg 21.49 r_dihedral_angle_3_deg 14.836 r_dihedral_angle_1_deg 5.934 r_angle_refined_deg 1.56 r_angle_other_deg 1.358 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3276 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing