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Crystal structure of the chromodomain-ATPase portion of the yeast Chd1 chromatin remodeler
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H1E PDB ENTRIES 2H1E,1Z63,1Z3I experimental model PDB 1Z63 PDB ENTRIES 2H1E,1Z63,1Z3I experimental model PDB 1Z3I PDB ENTRIES 2H1E,1Z63,1Z3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 18% PEG 3350;
400 mM K+/Na+ tartrate;
5% xylitol;
10 mM MgCl2;
1 mM ATPgammaS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.13 60.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.333 α = 90 b = 94.333 β = 90 c = 450.088 γ = 120
Symmetry Space Group P 61 2 2
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 ADSC QUANTUM 315 2008-03-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9792,0.9611 NSLS X29A
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 3.7 50 99.9 0.069 20.9 5.5 24026 20114 1 1
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 3.7 3.83 99.8 0.402 4.5 5.5
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT PDB ENTRIES 2H1E,1Z63,1Z3I 3.7 50 12949 12949 688 99.94 0.26462 0.26186 0.2648 0.31772 0.3241 RANDOM 126.878
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] 3.44 1.72 3.44 -5.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.411 r_dihedral_angle_3_deg 24.559 r_dihedral_angle_4_deg 20.41 r_dihedral_angle_1_deg 8.405 r_angle_refined_deg 1.628 r_chiral_restr 0.111 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.411 r_dihedral_angle_3_deg 24.559 r_dihedral_angle_4_deg 20.41 r_dihedral_angle_1_deg 8.405 r_angle_refined_deg 1.628 r_chiral_restr 0.111 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5712 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement SOLVE phasing SHARP phasing PHENIX refinement CBASS data collection HKL-2000 data reduction SCALEPACK data scaling