4O9I

Structure of CHD4 double chromodomains depicts cooperative folding for DNA binding


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72770.2M Ammonium citrate, 20% PEG3350, pH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8256.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.211α = 90
b = 60.475β = 90
c = 92.988γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-02-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97907APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.65099.10.0870.087253.992049204-370.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6499.60.6340.6342.44475

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.6508661866143599.170.213490.213490.211060.26373RANDOM56.179
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]
0.16-0.580.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.519
r_dihedral_angle_4_deg20.155
r_dihedral_angle_3_deg16.522
r_dihedral_angle_1_deg7.026
r_scangle_it4.78
r_angle_other_deg3.813
r_scbond_it3.099
r_mcangle_it1.732
r_angle_refined_deg1.642
r_mcbond_it0.836
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.519
r_dihedral_angle_4_deg20.155
r_dihedral_angle_3_deg16.522
r_dihedral_angle_1_deg7.026
r_scangle_it4.78
r_angle_other_deg3.813
r_scbond_it3.099
r_mcangle_it1.732
r_angle_refined_deg1.642
r_mcbond_it0.836
r_chiral_restr0.097
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_gen_planes_other0.009
r_bond_other_d
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1475
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345data collection
SERGUIdata collection
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
ARP/wARPmodel building
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
CCP4phasing