6PGE

WDR5delta32 bound to ethyl 3-(4-(hydroxymethyl)-1H-imidazol-2-yl)propanoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6PG4PDB entry 6PG4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2810.024 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 5.64, 26.3% w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.244.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.722α = 90
b = 65.18β = 90
c = 97.071γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95370Australian SynchrotronMX1

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
11.7646.7299.70.99713.47.130209
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)
11.761.7997.50.8752.97

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 6PG41.7635.3928628152499.510.183790.182250.21263RANDOM16.095
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]
-0.56-1.492.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_dihedral_angle_4_deg20.085
r_dihedral_angle_3_deg13.224
r_dihedral_angle_1_deg8.313
r_long_range_B_refined4.153
r_long_range_B_other4.152
r_angle_other_deg2.371
r_scangle_other2.163
r_mcangle_it1.471
r_mcangle_other1.471
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_dihedral_angle_4_deg20.085
r_dihedral_angle_3_deg13.224
r_dihedral_angle_1_deg8.313
r_long_range_B_refined4.153
r_long_range_B_other4.152
r_angle_other_deg2.371
r_scangle_other2.163
r_mcangle_it1.471
r_mcangle_other1.471
r_angle_refined_deg1.414
r_scbond_it1.381
r_scbond_other1.38
r_mcbond_it0.94
r_mcbond_other0.94
r_chiral_restr0.064
r_bond_other_d0.036
r_gen_planes_other0.01
r_bond_refined_d0.008
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 Atoms280
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing