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Structure of human MTHFD2 in complex with TH9028
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES pH 7.8, 80 % v/v MPD
Crystal Properties Matthews coefficient Solvent content 3.16 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.068 α = 90 b = 115.068 β = 90 c = 113.549 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 EIGER X 16M 2016-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA
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 1.95 49.3 99.9 13.5 10.2 62083
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 1.95 2
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 1.95 113.55 58965 3073 99.89 0.17013 0.16811 0.1817 0.21138 0.2285 RANDOM 58.736
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] 1.74 0.87 1.74 -5.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.08 r_dihedral_angle_4_deg 20.031 r_dihedral_angle_3_deg 13.677 r_long_range_B_refined 10.194 r_long_range_B_other 10.194 r_scangle_other 8.222 r_dihedral_angle_1_deg 6.082 r_scbond_it 5.771 r_scbond_other 5.77 r_mcangle_it 5.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.08 r_dihedral_angle_4_deg 20.031 r_dihedral_angle_3_deg 13.677 r_long_range_B_refined 10.194 r_long_range_B_other 10.194 r_scangle_other 8.222 r_dihedral_angle_1_deg 6.082 r_scbond_it 5.771 r_scbond_other 5.77 r_mcangle_it 5.106 r_mcangle_other 5.105 r_mcbond_it 3.818 r_mcbond_other 3.816 r_angle_refined_deg 1.809 r_angle_other_deg 1 r_chiral_restr 0.094 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 4483 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing