4X3U

Crystal structure of chromobox homolog 7 (CBX7) chromodomain with Suramin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52900.2 M lithium sulfate, 0.1 M Bis-Tris pH5.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.550.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.7α = 90
b = 58.7β = 90
c = 89.909γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A1NSLSX6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6322.6898.7848.218.720256

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.6322.6818956101698.780.163730.160120.2322RANDOM20.954
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]
0.070.07-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.594
r_sphericity_free33.744
r_sphericity_bonded15.702
r_dihedral_angle_4_deg14.13
r_dihedral_angle_3_deg12.135
r_dihedral_angle_1_deg7.054
r_rigid_bond_restr6.132
r_angle_refined_deg3.318
r_angle_other_deg1.732
r_chiral_restr0.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.594
r_sphericity_free33.744
r_sphericity_bonded15.702
r_dihedral_angle_4_deg14.13
r_dihedral_angle_3_deg12.135
r_dihedral_angle_1_deg7.054
r_rigid_bond_restr6.132
r_angle_refined_deg3.318
r_angle_other_deg1.732
r_chiral_restr0.797
r_gen_planes_other0.033
r_gen_planes_refined0.03
r_bond_refined_d0.028
r_bond_other_d0.012
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms946
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing