6PG3

WDR5delta23 bound to (2-butyl-1H-imidazol-4-yl)methanol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H9L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2810.182 M ammonium fluoride, 0.1 M sodium cacodylate (pH 5.79), 22.1 %w/v PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.2846.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.825α = 90
b = 46.85β = 112.81
c = 129.154γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95370Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.0443.6399.60.99410.37.439721
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.042.194.80.8662.77.2

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 REPLACEMENTTHROUGHOUT2H9L2.0443.6337833188799.570.174590.1730.20617RANDOM17.693
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]
1.940.10.04-1.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.762
r_dihedral_angle_4_deg20.201
r_dihedral_angle_3_deg13.881
r_dihedral_angle_1_deg8.263
r_long_range_B_refined4.119
r_long_range_B_other4.119
r_scangle_other2.573
r_angle_other_deg2.339
r_mcangle_it1.807
r_mcangle_other1.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.762
r_dihedral_angle_4_deg20.201
r_dihedral_angle_3_deg13.881
r_dihedral_angle_1_deg8.263
r_long_range_B_refined4.119
r_long_range_B_other4.119
r_scangle_other2.573
r_angle_other_deg2.339
r_mcangle_it1.807
r_mcangle_other1.806
r_scbond_it1.577
r_scbond_other1.577
r_angle_refined_deg1.392
r_mcbond_it1.123
r_mcbond_other1.122
r_chiral_restr0.06
r_bond_other_d0.036
r_bond_refined_d0.009
r_gen_planes_other0.009
r_gen_planes_refined0.006
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4650
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing