8VA5

Menin mutant - T349M in complex with Ziftomenib (KO-539)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GPQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2850.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Crystal Properties
Matthews coefficientSolvent content
2.2445.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.057α = 90
b = 80.034β = 90
c = 124.823γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2023-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.35098.90.13324.516.6120002
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3296.10.9812.034.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.326.344119911619398.7370.1620.16070.185813.487
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]
0.7280.372-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.414
r_dihedral_angle_2_deg13.412
r_dihedral_angle_3_deg11.748
r_dihedral_angle_1_deg5.858
r_lrange_it5.49
r_lrange_other5.489
r_scangle_it3.93
r_scangle_other3.929
r_dihedral_angle_other_2_deg3.923
r_scbond_it2.595
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3667
Nucleic Acid Atoms
Solvent Atoms634
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing