☰ Navigation Tabs
Human MTHFD2 in complex with compound 16a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 isopropanol, Bis-Tris pH 7.1, PEG 400, PEG 1000
Crystal Properties Matthews coefficient Solvent content 3.15 60.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.559 α = 90 b = 115.559 β = 90 c = 112.958 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 CCD RAYONIX MX300-HS 2019-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.54 30 98 0.065 12.8 2.9 27738
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 2.54 2.63 99.8 0.376 0.46 0.259 0.825 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.54 27.18 1.34 27684 1364 97.9 0.1942 0.1919 0.2397 0.222
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.161 f_angle_d 1.037 f_chiral_restr 0.057 f_plane_restr 0.01 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4389 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 164
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling HKL-2000 data reduction MOLREP phasing