3QMH

Structural Basis of Selective Binding of Non-Methylated CpG islands (DNA-TCGA) by the CXXC Domain of CFP1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QMB 

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.0740.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.458α = 90
b = 73.956β = 90
c = 124.062γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97924APS19-ID

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
12.51004683

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3QMB2.536.98468322894.720.207270.205960.23111RANDOM57.381
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]
0.23-0.07-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.154
r_dihedral_angle_4_deg22.792
r_dihedral_angle_3_deg16.805
r_dihedral_angle_1_deg7.883
r_scangle_it4.445
r_scbond_it3.018
r_mcangle_it1.777
r_angle_refined_deg1.098
r_mcbond_it1.054
r_chiral_restr0.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.154
r_dihedral_angle_4_deg22.792
r_dihedral_angle_3_deg16.805
r_dihedral_angle_1_deg7.883
r_scangle_it4.445
r_scbond_it3.018
r_mcangle_it1.777
r_angle_refined_deg1.098
r_mcbond_it1.054
r_chiral_restr0.064
r_gen_planes_refined0.015
r_bond_refined_d0.004
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms399
Nucleic Acid Atoms486
Solvent Atoms7
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement