3QMI

Structural Basis of Selective Binding of Non-Methylated CpG islands (DNA-ACGT) 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
2.1442.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.624α = 90
b = 75.009β = 90
c = 125.905γ = 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
12.11008362

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 REPLACEMENTTHROUGHOUT3QMB2.137.5836242099.20.2090.2070.258RANDOM19.21
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]
-0.170.130.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.595
r_dihedral_angle_4_deg16.281
r_dihedral_angle_3_deg14.193
r_dihedral_angle_1_deg8.157
r_scangle_it4.679
r_scbond_it3.559
r_mcangle_it2.231
r_mcbond_it1.564
r_angle_refined_deg1.361
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.595
r_dihedral_angle_4_deg16.281
r_dihedral_angle_3_deg14.193
r_dihedral_angle_1_deg8.157
r_scangle_it4.679
r_scbond_it3.559
r_mcangle_it2.231
r_mcbond_it1.564
r_angle_refined_deg1.361
r_chiral_restr0.078
r_gen_planes_refined0.022
r_bond_refined_d0.005
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 Atoms402
Nucleic Acid Atoms486
Solvent Atoms33
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement