6PGA

WDR5delta32 bound to methyl (4-(4-(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 DROP2810.237 M ammonium sulfate, 0.1 M bis-tris chloride, 25.7 %w/v MPEG5000
Crystal Properties
Matthews coefficientSolvent content
2.2144.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.782α = 90
b = 64.991β = 90
c = 97.386γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-08-16MSINGLE 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
12.4542.1799.90.985.912.411445
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)
12.452.5599.40.762212.8

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 REPLACEMENTTHROUGHOUT6PG42.4542.171084355699.830.199420.196720.25028RANDOM29.518
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]
1.95-4.022.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.237
r_dihedral_angle_4_deg19.852
r_dihedral_angle_3_deg14.598
r_dihedral_angle_1_deg7.931
r_long_range_B_refined4.378
r_long_range_B_other4.378
r_mcangle_it2.529
r_mcangle_other2.529
r_scangle_other2.526
r_angle_other_deg2.362
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.237
r_dihedral_angle_4_deg19.852
r_dihedral_angle_3_deg14.598
r_dihedral_angle_1_deg7.931
r_long_range_B_refined4.378
r_long_range_B_other4.378
r_mcangle_it2.529
r_mcangle_other2.529
r_scangle_other2.526
r_angle_other_deg2.362
r_mcbond_it1.507
r_mcbond_other1.506
r_scbond_it1.474
r_scbond_other1.471
r_angle_refined_deg1.39
r_chiral_restr0.049
r_bond_other_d0.036
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.005
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 Atoms74
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing