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Crystal structure of MAT2a with triazinone fragment 1 bound in the allosteric site
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 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.454 α = 90 b = 94.211 β = 90 c = 117.297 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 PILATUS 6M 2018-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.08 58.65 91.2 0.062 0.068 0.027 0.997 11.6 6.2 144857 9.86
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 1.08 1.11 52.4 0.948 1.093 0.529 0.626 3.9
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 1.08 58.64 144800 7307 90.9 0.168 0.167 0.165 0.183 0.1786 RANDOM 15.37
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] -3.8248 2.3867 1.4381
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.89 t_omega_torsion 5.1 t_angle_deg 1.1 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 14.89 t_omega_torsion 5.1 t_angle_deg 1.1 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 2916 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 40
Software Software Software Name Purpose Aimless data scaling AMoRE phasing BUSTER refinement PDB_EXTRACT data extraction DIALS data reduction