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Structure of human MTHFD2 in complex with TH9619
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES pH 7.6, 75 % v/v MPD
Crystal Properties Matthews coefficient Solvent content 3.25 62.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.895 α = 90 b = 116.895 β = 90 c = 112.965 γ = 120
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 2018-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.09 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 75.4 100 13.9 20.3 44494
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 75.4 42267 2131 99.89 0.18597 0.18395 0.1958 0.22534 0.2394 RANDOM 68.411
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] 2.12 1.06 2.12 -6.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.839 r_dihedral_angle_4_deg 21.391 r_dihedral_angle_3_deg 16.786 r_long_range_B_other 11.374 r_long_range_B_refined 11.373 r_scangle_other 8.885 r_mcangle_it 6.586 r_mcangle_other 6.585 r_dihedral_angle_1_deg 6.556 r_scbond_it 6.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.839 r_dihedral_angle_4_deg 21.391 r_dihedral_angle_3_deg 16.786 r_long_range_B_other 11.374 r_long_range_B_refined 11.373 r_scangle_other 8.885 r_mcangle_it 6.586 r_mcangle_other 6.585 r_dihedral_angle_1_deg 6.556 r_scbond_it 6.125 r_scbond_other 6.124 r_mcbond_it 4.859 r_mcbond_other 4.855 r_angle_refined_deg 1.702 r_angle_other_deg 1.034 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4444 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing