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Crystal structure of a HDAC-like protein with SAHA bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 NaCl, Na-cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.606 α = 90 b = 94.716 β = 104.75 c = 123.924 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97848 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.57 50
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.63 51.1
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 SAD THROUGHOUT 1.57 38.38 171414 9069 84.59 0.17366 0.17219 0.1691 0.20132 0.1986 RANDOM 16.498
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.726 r_dihedral_angle_4_deg 16.224 r_dihedral_angle_3_deg 12.406 r_dihedral_angle_1_deg 6.227 r_scangle_it 3.059 r_scbond_it 2.055 r_angle_refined_deg 1.456 r_mcangle_it 1.15 r_mcbond_it 0.708 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.726 r_dihedral_angle_4_deg 16.224 r_dihedral_angle_3_deg 12.406 r_dihedral_angle_1_deg 6.227 r_scangle_it 3.059 r_scbond_it 2.055 r_angle_refined_deg 1.456 r_mcangle_it 1.15 r_mcbond_it 0.708 r_nbtor_refined 0.31 r_metal_ion_refined 0.238 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10988 Nucleic Acid Atoms Solvent Atoms 1450 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing