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Crystal structure of fragment 3-(3-(pyridin-2-ylmethoxy)quinoxalin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.21 44.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.85 α = 90 b = 43.74 β = 90 c = 55.76 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN A200 A200 2016-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 1.55 29.85 99.2 0.025 0.027 0.01 1 69.9 6.8 14896
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 1.55 1.58 95.6 0.083 0.091 0.036 0.996 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.55 29.85 14173 722 98.96 0.1437 0.1427 0.155 0.1621 0.169 RANDOM 9.957
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] -0.33 0.76 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.841 r_dihedral_angle_3_deg 11.504 r_dihedral_angle_1_deg 6.376 r_angle_refined_deg 1.541 r_angle_other_deg 1.091 r_chiral_restr 0.113 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 775 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PDB_EXTRACT data extraction Aimless data scaling