8XAM

Co-crystal structure of compound 7 in complex with MAT2A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UGH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2970.2 M LiCl, 0.1 M Tris pH 8.0, (18%-20%) PEG6000, 10% Ethylene Glycol
Crystal Properties
Matthews coefficientSolvent content
2.2244.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.968α = 90
b = 94.043β = 90
c = 116.892γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 18-ID1.1807APS18-ID

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
11.347.0294.1125.96.9169065
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)
11.31.320.931

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 REPLACEMENTFREE R-VALUE1.340.119169062842693.9480.1220.12130.142711.625
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]
0.4910.014-0.241-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.957
r_dihedral_angle_4_deg21.015
r_dihedral_angle_3_deg11.373
r_dihedral_angle_1_deg6.882
r_lrange_it5.304
r_lrange_other4.834
r_scangle_it3.184
r_scangle_other3.183
r_scbond_it2.157
r_scbond_other2.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.957
r_dihedral_angle_4_deg21.015
r_dihedral_angle_3_deg11.373
r_dihedral_angle_1_deg6.882
r_lrange_it5.304
r_lrange_other4.834
r_scangle_it3.184
r_scangle_other3.183
r_scbond_it2.157
r_scbond_other2.157
r_angle_refined_deg1.999
r_angle_other_deg1.595
r_mcangle_it1.462
r_mcangle_other1.462
r_mcbond_it1.007
r_mcbond_other1.007
r_xyhbond_nbd_refined0.283
r_symmetry_xyhbond_nbd_other0.236
r_nbd_refined0.233
r_symmetry_xyhbond_nbd_refined0.232
r_nbd_other0.204
r_symmetry_nbd_other0.19
r_nbtor_refined0.178
r_symmetry_nbd_refined0.119
r_chiral_restr0.118
r_symmetry_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.014
r_gen_planes_other0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5882
Nucleic Acid Atoms
Solvent Atoms1098
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing