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The structure of HDAC1 in complex with the dimeric ELM2-SANT domain of MTA1 from the NuRD complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A69 PDB ENTRY 4A69
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M NA HEPES PH7.5, 2M AMMONIUM SULPHATE, 5% PEG400
Crystal Properties Matthews coefficient Solvent content 3.71 66.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.199 α = 90 b = 108.199 β = 90 c = 133.164 γ = 120
Symmetry Space Group P 32 2 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 2011-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 3 76.6 96.7 0.16 6 3 16916 1.8
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 3 3.18 97.6 0.66 3.1 3.1
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 4A69 3 76.75 16916 910 96.12 0.21337 0.21084 0.2107 0.26149 0.2608 RANDOM 53.23
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] 0.5 0.5 0.5 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.692 r_dihedral_angle_4_deg 18.694 r_dihedral_angle_3_deg 16.653 r_dihedral_angle_1_deg 6.83 r_angle_refined_deg 1.023 r_chiral_restr 0.068 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.692 r_dihedral_angle_4_deg 18.694 r_dihedral_angle_3_deg 16.653 r_dihedral_angle_1_deg 6.83 r_angle_refined_deg 1.023 r_chiral_restr 0.068 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4235 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PHASER phasing