3UVK

Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H13PDB ENTRY 2H13

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.53230.1 M ammonium sulfate, 24% PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K
Crystal Properties
Matthews coefficientSolvent content
2.0439.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.827α = 90
b = 68.496β = 90
c = 87.815γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 300 mm CCD2011-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12718APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.431.90798.30.04147.46.8558495776622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4581.90.3552.74.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 2H131.431.9072558495473229170.153390.151360.19242RANDOM14.34
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]
0.160.11-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.136
r_dihedral_angle_4_deg25.715
r_dihedral_angle_3_deg13.038
r_dihedral_angle_1_deg7.741
r_scangle_it7.296
r_scbond_it5.249
r_mcangle_it3.709
r_rigid_bond_restr2.848
r_mcbond_it2.69
r_angle_refined_deg2.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.136
r_dihedral_angle_4_deg25.715
r_dihedral_angle_3_deg13.038
r_dihedral_angle_1_deg7.741
r_scangle_it7.296
r_scbond_it5.249
r_mcangle_it3.709
r_rigid_bond_restr2.848
r_mcbond_it2.69
r_angle_refined_deg2.206
r_chiral_restr0.161
r_bond_refined_d0.027
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2392
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms19

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling