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Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), PLP-internal aldimine and apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 55% Tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.5 50.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.657 α = 90 b = 201.563 β = 90 c = 64.782 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX300-HS 2017-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.74 90 99.6 0.056 0.063 16.7 4.5 203236
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.84 98.5 0.93 1.06 1.9 4.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6CCZ 1.74 83.94 202206 1017 99.6 0.175 0.175 0.219 0.2088 RANDOM 33.125
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] 0.81 -1.71 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.988 r_dihedral_angle_4_deg 15.666 r_dihedral_angle_3_deg 13.002 r_long_range_B_refined 6.442 r_long_range_B_other 6.441 r_dihedral_angle_1_deg 6.323 r_scangle_other 1.749 r_mcangle_it 1.529 r_mcangle_other 1.529 r_angle_refined_deg 1.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.988 r_dihedral_angle_4_deg 15.666 r_dihedral_angle_3_deg 13.002 r_long_range_B_refined 6.442 r_long_range_B_other 6.441 r_dihedral_angle_1_deg 6.323 r_scangle_other 1.749 r_mcangle_it 1.529 r_mcangle_other 1.529 r_angle_refined_deg 1.427 r_scbond_it 1.029 r_scbond_other 1.029 r_angle_other_deg 0.954 r_mcbond_it 0.87 r_mcbond_other 0.868 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 13917 Nucleic Acid Atoms Solvent Atoms 1409 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing