2B2V

Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MeK4


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
182834% 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
Matthew coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.255α = 90
b = 54.177β = 111.97
c = 99.96γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.530.994.80.08516.33.618233
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5971.70.4851.352.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY B2T WITHOUT CHAIN D2.6530.9182331614678998.10.2160.2130.266RANDOM48.77
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]
-6.68-2.76.29-1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.948
r_dihedral_angle_4_deg24.459
r_dihedral_angle_3_deg22.463
r_dihedral_angle_1_deg8.686
r_scangle_it7.51
r_scbond_it5.574
r_mcangle_it3.56
r_mcbond_it2.636
r_angle_refined_deg1.709
r_angle_other_deg1.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.948
r_dihedral_angle_4_deg24.459
r_dihedral_angle_3_deg22.463
r_dihedral_angle_1_deg8.686
r_scangle_it7.51
r_scbond_it5.574
r_mcangle_it3.56
r_mcbond_it2.636
r_angle_refined_deg1.709
r_angle_other_deg1.107
r_mcbond_other0.702
r_symmetry_vdw_other0.566
r_symmetry_vdw_refined0.53
r_chiral_restr0.332
r_nbd_refined0.33
r_nbd_other0.303
r_symmetry_hbond_refined0.284
r_nbtor_refined0.223
r_xyhbond_nbd_refined0.215
r_xyhbond_nbd_other0.13
r_nbtor_other0.107
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_symmetry_metal_ion_other
r_metal_ion_other
r_metal_ion_refined
r_symmetry_metal_ion_refined
r_gen_planes_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3556
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data scaling
MOLREPphasing