2P2R

Crystal structure of the third KH domain of human Poly(C)-Binding Protein-2 in complex with C-rich strand of human telomeric DNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.182952M ammonium sulfate, 80 mM lithium sulfate, 100 mM CAPS, pH 8.18, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7855.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.069α = 90
b = 81.069β = 90
c = 87.815γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210KOHZU: Double Crystal Si(111)2006-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11588, 0.97945ALS8.3.1

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
11.654.898.50.0330.03622.86.8157521551622
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)
1.61.64284.660.4060.3827.33.6

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 DIFFRACTIONSADTHROUGHOUT1.654.81384272398.040.20660.204820.24225RANDOM28.797
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]
0.490.240.49-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.648
r_dihedral_angle_4_deg23.314
r_dihedral_angle_3_deg10.647
r_dihedral_angle_1_deg4.443
r_scangle_it3.661
r_scbond_it2.71
r_mcangle_it2.225
r_mcbond_it1.559
r_angle_refined_deg1.349
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.648
r_dihedral_angle_4_deg23.314
r_dihedral_angle_3_deg10.647
r_dihedral_angle_1_deg4.443
r_scangle_it3.661
r_scbond_it2.71
r_mcangle_it2.225
r_mcbond_it1.559
r_angle_refined_deg1.349
r_nbtor_refined0.301
r_nbd_refined0.205
r_symmetry_hbond_refined0.178
r_symmetry_vdw_refined0.125
r_xyhbond_nbd_refined0.124
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms569
Nucleic Acid Atoms137
Solvent Atoms81
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSphasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling