2O9K

WDR5 in Complex with Dimethylated H3K4 Peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.530020% PEG 5000 MME, 0.1M BIS-TRIS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.244.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.045α = 90
b = 46.975β = 117.26
c = 112.236γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2006-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.910096.447729
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9776

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.910045288242996.20.1770.1740.226RANDOM21.56
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]
0.03-0.22-0.350.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.44
r_dihedral_angle_4_deg20.209
r_dihedral_angle_3_deg14.267
r_dihedral_angle_1_deg7.483
r_scangle_it2.634
r_scbond_it1.796
r_angle_refined_deg1.352
r_mcangle_it1.112
r_mcbond_it0.694
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.44
r_dihedral_angle_4_deg20.209
r_dihedral_angle_3_deg14.267
r_dihedral_angle_1_deg7.483
r_scangle_it2.634
r_scbond_it1.796
r_angle_refined_deg1.352
r_mcangle_it1.112
r_mcbond_it0.694
r_nbtor_refined0.295
r_nbd_refined0.19
r_symmetry_vdw_refined0.172
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.136
r_chiral_restr0.09
r_bond_refined_d0.013
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 Atoms4817
Nucleic Acid Atoms
Solvent Atoms615
Heterogen Atoms

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
CrystalCleardata reduction
DENZOdata reduction
SCALEPACKdata scaling