2VPB

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8292HANGING-DROP VAPOUR-DIFFUSION METHOD AT 19 CELSIUS. CRYSTALLIZATION CONDITIONS: 1M NA-CITRATE, 100MM TRIS PH7, 200MM NACL, pH 8
Crystal Properties
Matthews coefficientSolvent content
2.5351.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.1α = 90
b = 79.47β = 90
c = 91.83γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL FOCUSING MIRROR2007-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.5928.5699.90.0626.610.5154262
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.6899.90.3711.410.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2VP71.5960.081542681499.80.1940.1920.225RANDOM22.93
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]
1.3-0.49-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.242
r_dihedral_angle_4_deg14.161
r_dihedral_angle_3_deg12.993
r_dihedral_angle_1_deg5.503
r_scangle_it3.613
r_scbond_it2.235
r_mcangle_it1.477
r_angle_refined_deg1.147
r_mcbond_it0.78
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.242
r_dihedral_angle_4_deg14.161
r_dihedral_angle_3_deg12.993
r_dihedral_angle_1_deg5.503
r_scangle_it3.613
r_scbond_it2.235
r_mcangle_it1.477
r_angle_refined_deg1.147
r_mcbond_it0.78
r_nbtor_refined0.298
r_symmetry_vdw_refined0.221
r_nbd_refined0.208
r_symmetry_hbond_refined0.13
r_xyhbond_nbd_refined0.123
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_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 Atoms690
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing