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Tandem chromodomains of budding yeast CHD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B2Y PDB ENTRY 2B2Y, CHAIN A WITHOUT B1-B2 LOOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 283 10mM BTP, 12mM NaCl, 5mM TCEP, 0.9M ammonium sulfate, 3.75% isopropanol, 4.5mg/ml yeast CHD1 tandem chromodomains, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
Crystal Properties Matthews coefficient Solvent content 3.11 60.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.185 α = 90 b = 136.185 β = 90 c = 57.516 γ = 90
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 2005-07-12 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 2.2 19.57 95.7 0.104 10.8 3.5 25838 -3
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 2.2 2.28 80.9 0.449 1.7 2
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2B2Y, CHAIN A WITHOUT B1-B2 LOOP 2.2 19.57 25934 25796 1299 95.7 0.192 0.189 0.1936 0.246 0.248 RANDOM 30.85
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.941 r_dihedral_angle_1_deg 28.126 r_dihedral_angle_4_deg 20.282 r_dihedral_angle_3_deg 17.408 r_scangle_it 6.189 r_scbond_it 4.383 r_mcangle_it 2.338 r_mcbond_it 2.25 r_angle_refined_deg 2.226 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.941 r_dihedral_angle_1_deg 28.126 r_dihedral_angle_4_deg 20.282 r_dihedral_angle_3_deg 17.408 r_scangle_it 6.189 r_scbond_it 4.383 r_mcangle_it 2.338 r_mcbond_it 2.25 r_angle_refined_deg 2.226 r_nbtor_refined 0.318 r_nbd_refined 0.273 r_chiral_restr 0.266 r_symmetry_vdw_refined 0.266 r_xyhbond_nbd_refined 0.246 r_symmetry_hbond_refined 0.223 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 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_refined 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 2740 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction