6PG5

WDR5delta32 bound to benzyl (4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6PG4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2810.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.2144.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.65α = 90
b = 65.204β = 90
c = 97.477γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-04-28MSINGLE 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
11.9948.7498.50.99817.27.320794
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)
11.992.04950.9465.87.2

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 REPLACEMENTTHROUGHOUT6PG41.9942.1119707104998.230.158980.156740.20159RANDOM12.663
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]
0.02-0.930.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.454
r_dihedral_angle_4_deg17.323
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg8.24
r_long_range_B_refined3.898
r_long_range_B_other3.897
r_angle_other_deg2.374
r_scangle_other1.897
r_angle_refined_deg1.395
r_mcangle_it1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.454
r_dihedral_angle_4_deg17.323
r_dihedral_angle_3_deg13.523
r_dihedral_angle_1_deg8.24
r_long_range_B_refined3.898
r_long_range_B_other3.897
r_angle_other_deg2.374
r_scangle_other1.897
r_angle_refined_deg1.395
r_mcangle_it1.27
r_mcangle_other1.27
r_scbond_it1.174
r_scbond_other1.15
r_mcbond_it0.77
r_mcbond_other0.769
r_chiral_restr0.063
r_bond_other_d0.036
r_bond_refined_d0.009
r_gen_planes_other0.009
r_gen_planes_refined0.007
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 Atoms2360
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing