2VPE

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292HANGING-DROP VAPOUR-DIFFUSION METHOD AT 19 CELSIUS. 26.4% PEG-3350, 200MM LISO4, 100MM TRIS PH7
Crystal Properties
Matthews coefficientSolvent content
3.160.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.72α = 90
b = 105.72β = 90
c = 51.43γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDKIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING2007-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.742.371000.1212.410.3309942
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)
11.71.791001.212.210.2

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 2VPB1.710630994165599.90.1950.1930.23RANDOM28.81
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]
0.640.64-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.458
r_dihedral_angle_4_deg17.174
r_dihedral_angle_3_deg11.476
r_dihedral_angle_1_deg5.669
r_scangle_it3.642
r_scbond_it2.252
r_mcangle_it1.567
r_angle_refined_deg1.197
r_mcbond_it0.921
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.458
r_dihedral_angle_4_deg17.174
r_dihedral_angle_3_deg11.476
r_dihedral_angle_1_deg5.669
r_scangle_it3.642
r_scbond_it2.252
r_mcangle_it1.567
r_angle_refined_deg1.197
r_mcbond_it0.921
r_nbtor_refined0.299
r_nbd_refined0.199
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.125
r_symmetry_hbond_refined0.116
r_chiral_restr0.088
r_bond_refined_d0.011
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 Atoms1454
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing