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Crystal structure of D101L Fe2+ HDAC8 complexed with M344
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 298 Drop composition: 25 mM Tris, 2.5% glycerol, 75 mM KCl, 10-18% PEG 35K, 50 mM MES, 1 mM tri(2-carboxyethyl)phosphine (TCEP), 0.03 mM gly-gly-gly, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.616 α = 90 b = 87.561 β = 90 c = 52.488 γ = 90
Symmetry Space Group P 21 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 93 CCD ADSC QUANTUM 315 2009-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.0720 APS 24-ID-C
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 50 98.7 0.064 28.1 6.6 53795 28881 36
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) 2 2.07 90.5 0.254 5.2 4.9 2586
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 MOLECULAR REPLACEMENT THROUGHOUT 2 50 27381 1457 98.59 0.20225 0.1999 0.1992 0.24733 0.2442 RANDOM 32.763
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] 2.62 -0.14 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.72 r_dihedral_angle_4_deg 19.236 r_dihedral_angle_3_deg 15.883 r_dihedral_angle_1_deg 6.397 r_scangle_it 5.58 r_scbond_it 3.547 r_mcangle_it 2.244 r_angle_refined_deg 1.419 r_mcbond_it 1.327 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.72 r_dihedral_angle_4_deg 19.236 r_dihedral_angle_3_deg 15.883 r_dihedral_angle_1_deg 6.397 r_scangle_it 5.58 r_scbond_it 3.547 r_mcangle_it 2.244 r_angle_refined_deg 1.419 r_mcbond_it 1.327 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2784 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 25
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling