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Mutant S-adenosylmethionine synthetase from E.coli complexed with AMPPNP and methionine
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 0.2M L-Proline
0.1M Hepes pH 7.56
14% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.99 38.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.611 α = 90 b = 86.611 β = 90 c = 90.982 γ = 90
Symmetry Space Group P 42 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 PIXEL DECTRIS EIGER2 X 16M 2021-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
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 1.6 62.73 99.96 0.083 1 26.2 45.8 46194 31.66
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 1.6 1.658 4.035 0.4 0.4
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 1P7L 1.6 62.73 43830 2366 99.97 0.18391 0.18193 0.2196 0.1988 RANDOM 36.14
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] 0.17 0.17 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.321 r_dihedral_angle_3_deg 15.198 r_dihedral_angle_4_deg 13.155 r_dihedral_angle_1_deg 7.179 r_long_range_B_other 6.243 r_long_range_B_refined 6.236 r_scangle_other 4.652 r_scbond_it 3.084 r_scbond_other 3.084 r_mcangle_it 2.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.321 r_dihedral_angle_3_deg 15.198 r_dihedral_angle_4_deg 13.155 r_dihedral_angle_1_deg 7.179 r_long_range_B_other 6.243 r_long_range_B_refined 6.236 r_scangle_other 4.652 r_scbond_it 3.084 r_scbond_other 3.084 r_mcangle_it 2.96 r_mcangle_other 2.96 r_mcbond_it 2.134 r_mcbond_other 2.131 r_angle_refined_deg 2.013 r_angle_other_deg 1.512 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 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 2895 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing