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Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BZ6 PDB ENTRY 4BZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M NA,K L-TARTRATE, 21% (W/V) PEG3350
Crystal Properties Matthews coefficient Solvent content 1.5 19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.778 α = 77.79 b = 70.815 β = 75.45 c = 98.024 γ = 85.4
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RIGAKU SATURN 944 2011-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.3 50 96.3 0.11 15.2 3.8 80076 2 33.74
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 2.3 2.34 93.8 0.34 4.2 3.8
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 (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 PDB ENTRY 4BZ6 2.3 32.89 79759 4044 99.76 0.1922 0.19 0.1868 0.2323 0.23 RANDOM 26.65
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] 0.8676 -0.7132 -0.5091 -1.8136 1.0778 0.9459
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.89 t_omega_torsion 2.95 t_angle_deg 1.02 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.89 t_omega_torsion 2.95 t_angle_deg 1.02 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13004 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 185
Software Software Software Name Purpose BUSTER refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing