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S-adenosylmethionine synthetase from Lactobacillus plantarum complexed with AMPPNP, methionine and SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P7L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 50mM CaCl2
0.1M Bis-Tris pH 6.8
32.14% PEG MME 550
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.426 α = 93.82 b = 110.927 β = 104.03 c = 112.661 γ = 99.59
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 S 16M 2019-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.82 29.39 94.6 0.114 0.996 10.2 3.5 61578 65.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.921 0.7 0.706 1.6
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 1P7L 2.82 29.41 58472 3108 94.93 0.16143 0.15563 0.1533 0.27492 0.2735 RANDOM 68.045
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] -2.92 -4.73 0.58 -6.27 -1.77 9.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.338 r_dihedral_angle_4_deg 22.277 r_dihedral_angle_3_deg 18.475 r_long_range_B_other 13.343 r_long_range_B_refined 13.34 r_scangle_other 11.997 r_mcangle_other 10.945 r_mcangle_it 10.943 r_scbond_it 9.129 r_scbond_other 9.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.338 r_dihedral_angle_4_deg 22.277 r_dihedral_angle_3_deg 18.475 r_long_range_B_other 13.343 r_long_range_B_refined 13.34 r_scangle_other 11.997 r_mcangle_other 10.945 r_mcangle_it 10.943 r_scbond_it 9.129 r_scbond_other 9.112 r_mcbond_it 8.322 r_mcbond_other 8.314 r_dihedral_angle_1_deg 7.725 r_rigid_bond_restr 3.237 r_angle_refined_deg 1.546 r_angle_other_deg 1.223 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22380 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 273
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing