6PG7

WDR5delta32 bound to (2-(3-methoxy-3-phenylpropyl)-1H-imidazol-4-yl)methanol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2810.17 M ammonium sulfate, 0.1 bis-tris chloride (pH 6.3), 30.5 %w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.2244.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.963α = 90
b = 65.303β = 90
c = 97.307γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-07-09MSINGLE 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
12.4548.6599.70.99713.16.911523
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)
12.452.5597.60.8082.46.8

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 REPLACEMENTTHROUGHOUT6PG42.4548.651094553699.670.197910.195590.24305RANDOM37.873
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]
3.5-4.480.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.168
r_dihedral_angle_4_deg25.902
r_dihedral_angle_3_deg14.803
r_dihedral_angle_1_deg8.264
r_long_range_B_refined6.809
r_long_range_B_other6.809
r_scangle_other3.505
r_mcangle_it3.309
r_mcangle_other3.308
r_angle_other_deg2.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.168
r_dihedral_angle_4_deg25.902
r_dihedral_angle_3_deg14.803
r_dihedral_angle_1_deg8.264
r_long_range_B_refined6.809
r_long_range_B_other6.809
r_scangle_other3.505
r_mcangle_it3.309
r_mcangle_other3.308
r_angle_other_deg2.344
r_scbond_it2.154
r_scbond_other2.153
r_mcbond_it2.059
r_mcbond_other2.056
r_angle_refined_deg1.403
r_chiral_restr0.06
r_bond_other_d0.036
r_bond_refined_d0.008
r_gen_planes_other0.007
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 Atoms2360
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing