☰ Navigation Tabs
Structure of the pathogenic variant G423S of Human SHMT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 MORPHEUS screen (Molecular Dimensions) condition D4
Crystal Properties Matthews coefficient Solvent content 2.39 48.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.339 α = 90 b = 126.009 β = 90 c = 135.26 γ = 90
Symmetry Space Group P 21 21 21
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 2021-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0000 ELETTRA 11.2C
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 1.8 46.1 99.9 0.125 0.135 0.038 0.999 11.3 12.7 191505
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 1.8 1.83 1.432 1.555 0.445 0.863 12.1
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 1.8 46.1 181829 9508 99.91 0.23912 0.23813 0.2456 0.25768 0.2626 RANDOM 33.861
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] 5.95 -2.76 -3.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.919 r_dihedral_angle_2_deg 12.139 r_long_range_B_refined 7.324 r_long_range_B_other 7.301 r_dihedral_angle_1_deg 6.599 r_scangle_other 5.835 r_mcangle_it 4.142 r_mcangle_other 4.142 r_scbond_it 3.768 r_scbond_other 3.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.919 r_dihedral_angle_2_deg 12.139 r_long_range_B_refined 7.324 r_long_range_B_other 7.301 r_dihedral_angle_1_deg 6.599 r_scangle_other 5.835 r_mcangle_it 4.142 r_mcangle_other 4.142 r_scbond_it 3.768 r_scbond_other 3.767 r_mcbond_it 2.934 r_mcbond_other 2.934 r_angle_refined_deg 1.74 r_angle_other_deg 0.624 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 14022 Nucleic Acid Atoms Solvent Atoms 786 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction