6OI2

Crystal structure of human WDR5 in complex with symmetric dimethyl-L-arginine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H14 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.9295100 mM Bis-Tris pH5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 0.66 mM symmetric dimethyl-L-arginine
Crystal Properties
Matthews coefficientSolvent content
2.140

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.053α = 90
b = 86.285β = 90
c = 40.865γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEKB mirrors2018-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.6859.0899.80.0315.77.233411

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 REPLACEMENTTHROUGHOUT2H141.6859.0831626169599.540.183350.181310.22285RANDOM26.174
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]
-2.1-0.252.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.461
r_dihedral_angle_4_deg14.924
r_dihedral_angle_3_deg12.138
r_dihedral_angle_1_deg7.642
r_long_range_B_refined4.646
r_long_range_B_other4.645
r_scangle_other2.984
r_mcangle_it2.02
r_mcangle_other2.02
r_scbond_it1.894
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.461
r_dihedral_angle_4_deg14.924
r_dihedral_angle_3_deg12.138
r_dihedral_angle_1_deg7.642
r_long_range_B_refined4.646
r_long_range_B_other4.645
r_scangle_other2.984
r_mcangle_it2.02
r_mcangle_other2.02
r_scbond_it1.894
r_scbond_other1.89
r_angle_refined_deg1.435
r_mcbond_it1.35
r_mcbond_other1.342
r_angle_other_deg0.91
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms2339
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing