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Structure of the pathogenic variant P157S of Human SHMT2 in a distorted tetrameric conformation
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 C4
Crystal Properties Matthews coefficient Solvent content 3.64 66.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.134 α = 90 b = 162.134 β = 90 c = 207.382 γ = 120
Symmetry Space Group P 65 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 EIGER2 X 9M 2021-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.0596 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 140.41 100 0.202 0.999 14.2 21.3 44777
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 2.093 0.722 1.8
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 2.7 140.41 42416 2296 99.98 0.25485 0.2546 0.257 0.25943 0.2629 RANDOM 67.094
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] 1.32 0.66 1.32 -4.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.42 r_long_range_B_refined 7.998 r_long_range_B_other 7.998 r_dihedral_angle_2_deg 7.018 r_dihedral_angle_1_deg 5.804 r_scangle_other 5.24 r_mcangle_it 4.943 r_mcangle_other 4.943 r_mcbond_it 3.097 r_mcbond_other 3.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.42 r_long_range_B_refined 7.998 r_long_range_B_other 7.998 r_dihedral_angle_2_deg 7.018 r_dihedral_angle_1_deg 5.804 r_scangle_other 5.24 r_mcangle_it 4.943 r_mcangle_other 4.943 r_mcbond_it 3.097 r_mcbond_other 3.096 r_scbond_it 3.073 r_scbond_other 3.064 r_angle_refined_deg 1.009 r_angle_other_deg 0.332 r_chiral_restr 0.042 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 6741 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction