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Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), in complex with glycine, PLP and folate-competitive pyrazolopyran inhibitor: 6-amino-4-isopropyl-3-methyl-4-(3-(pyrrolidin-1-yl)-5-(trifluoromethyl)phenyl)-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile
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, HANGING DROP 8.5 277 0.1 M TRIS ph 8.5, 17% (w/v) PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.66 66.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.14 α = 90 b = 160.14 β = 90 c = 210.1 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 CCD MARMOSAIC 300 mm CCD 2015-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
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 2.47 83.74 100 18.04 10.91 57441
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4PVF 2.47 80 52776 2775 96.7 0.204 0.20226 0.2062 0.23752 0.2424 RANDOM 51.733
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 -4.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.85 r_dihedral_angle_4_deg 13.952 r_dihedral_angle_3_deg 13.184 r_long_range_B_refined 6.218 r_long_range_B_other 6.218 r_dihedral_angle_1_deg 5.871 r_mcangle_other 3.266 r_mcangle_it 3.265 r_scangle_other 2.922 r_mcbond_other 1.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.85 r_dihedral_angle_4_deg 13.952 r_dihedral_angle_3_deg 13.184 r_long_range_B_refined 6.218 r_long_range_B_other 6.218 r_dihedral_angle_1_deg 5.871 r_mcangle_other 3.266 r_mcangle_it 3.265 r_scangle_other 2.922 r_mcbond_other 1.874 r_mcbond_it 1.873 r_scbond_it 1.621 r_scbond_other 1.62 r_angle_refined_deg 1.238 r_angle_other_deg 0.889 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 7246 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement XDS data processing PHASER phasing Coot model building