4ER5

Crystal structure of human DOT1L in complex with 2 molecules of EPZ004777


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52933.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.766.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.605α = 90
b = 150.605β = 90
c = 53.179γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.979310APS31-ID

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
12.5749.2431000.09421.2112227722277
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.572.711000.9390.9390.711.33231

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.5749.242226722247110099.910.19640.19640.19530.2177PDB entry 3qow52.7349
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]
-0.52-0.26-0.520.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.011
r_dihedral_angle_4_deg15.913
r_dihedral_angle_3_deg13.989
r_dihedral_angle_1_deg5.683
r_scangle_it2.757
r_scbond_it1.624
r_angle_refined_deg1.307
r_mcangle_it1.253
r_angle_other_deg0.871
r_mcbond_it0.659
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.011
r_dihedral_angle_4_deg15.913
r_dihedral_angle_3_deg13.989
r_dihedral_angle_1_deg5.683
r_scangle_it2.757
r_scbond_it1.624
r_angle_refined_deg1.307
r_mcangle_it1.253
r_angle_other_deg0.871
r_mcbond_it0.659
r_mcbond_other0.092
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2535
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms83

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
31IDdata collection
XSCALEdata scaling