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Crystal structure of MAT2a bound to allosteric inhibitor and in vivo tool compound 28
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 8-12 % PEG8000, 8-12 % ethylene glycol, 0.1 M HEPES pH 8.0; soaked with 0.01 M compound (10 % DMSO)
Crystal Properties Matthews coefficient Solvent content 2.13 42.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.176 α = 90 b = 93.853 β = 90 c = 117.069 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.16 73.226 92.2 0.032 0.035 0.014 0.999 27.4 5.6 118866 9.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.16 1.198 50.4 0.115 0.15 0.095 0.98 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT internal model 1.16 16.93 118866 5930 91.9 0.149 0.149 0.1449 0.157 0.1567 RANDOM 12.8
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] 0.1436 -0.0108 -0.1327
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.63 t_omega_torsion 5.52 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.63 t_omega_torsion 5.52 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2923 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 48
Software Software Software Name Purpose XDS data reduction STARANISO data scaling BUSTER refinement PDB_EXTRACT data extraction AMoRE phasing