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Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MeK4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B2T WITHOUT CHAIN D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 283 4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.255 α = 90 b = 54.177 β = 111.97 c = 99.96 γ = 90
Symmetry Space Group C 1 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 CCD MARRESEARCH 2005-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 30.9 94.8 0.085 16.3 3.6 18233
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 71.7 0.485 1.35 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY B2T WITHOUT CHAIN D 2.65 30.9 18233 16146 789 98.1 0.216 0.213 0.2189 0.266 RANDOM 48.77
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] -6.68 -2.7 6.29 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.948 r_dihedral_angle_4_deg 24.459 r_dihedral_angle_3_deg 22.463 r_dihedral_angle_1_deg 8.686 r_scangle_it 7.51 r_scbond_it 5.574 r_mcangle_it 3.56 r_mcbond_it 2.636 r_angle_refined_deg 1.709 r_angle_other_deg 1.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.948 r_dihedral_angle_4_deg 24.459 r_dihedral_angle_3_deg 22.463 r_dihedral_angle_1_deg 8.686 r_scangle_it 7.51 r_scbond_it 5.574 r_mcangle_it 3.56 r_mcbond_it 2.636 r_angle_refined_deg 1.709 r_angle_other_deg 1.107 r_mcbond_other 0.702 r_symmetry_vdw_other 0.566 r_symmetry_vdw_refined 0.53 r_chiral_restr 0.332 r_nbd_refined 0.33 r_nbd_other 0.303 r_symmetry_hbond_refined 0.284 r_nbtor_refined 0.223 r_xyhbond_nbd_refined 0.215 r_xyhbond_nbd_other 0.13 r_nbtor_other 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3556 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data scaling MOLREP phasing