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Structure of the pathogenic variant P157S of Human SHMT2 in the apo open dimeric conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 MoORPHEUS screen (Molecular Dimensions) condition F9
Crystal Properties Matthews coefficient Solvent content 2.3 46.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.716 α = 90 b = 74.153 β = 108.9 c = 74.349 γ = 90
Symmetry Space Group C 1 2 1
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 2.658 57.2 95.1 0.075 0.995 11.9 3.2 13465 65.19
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 2.658 2.704 0.465 0.746 2.1 1.9
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 2.658 57.19 12814 651 95.06 0.20829 0.20538 0.2123 0.26411 0.264 RANDOM 76.774
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] -3.09 2.67 1.03 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.294 r_long_range_B_refined 13.55 r_long_range_B_other 13.549 r_scangle_other 9.319 r_mcangle_it 7.585 r_mcangle_other 7.583 r_dihedral_angle_2_deg 7.239 r_dihedral_angle_1_deg 6.345 r_scbond_it 5.788 r_scbond_other 5.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.294 r_long_range_B_refined 13.55 r_long_range_B_other 13.549 r_scangle_other 9.319 r_mcangle_it 7.585 r_mcangle_other 7.583 r_dihedral_angle_2_deg 7.239 r_dihedral_angle_1_deg 6.345 r_scbond_it 5.788 r_scbond_other 5.786 r_mcbond_it 4.925 r_mcbond_other 4.925 r_angle_refined_deg 1.208 r_angle_other_deg 0.42 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 3250 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction