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Human Methionine Adenosyltransferase II mutant (P115G)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1M HEPES
35% PEG600
Crystal Properties Matthews coefficient Solvent content 2.21 44.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.33 α = 90 b = 94.87 β = 90 c = 117.37 γ = 90
Symmetry Space Group I 2 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 PIXEL DECTRIS PILATUS3 6M 2017-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.7 54.36 86.7 0.162 0.197 0.111 0.979 5.2 4.4 8945
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 89.6 0.564 0.693 0.397 0.566 2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5a1i 2.7 54.36 8483 458 85.01 0.1942 0.19195 0.197 0.23407 0.2364 RANDOM 48.785
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] 4.31 -2.6 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.088 r_dihedral_angle_3_deg 15.995 r_dihedral_angle_4_deg 13.541 r_long_range_B_refined 7.838 r_long_range_B_other 7.838 r_dihedral_angle_1_deg 7.432 r_mcangle_it 4.322 r_mcangle_other 4.321 r_scangle_other 4.284 r_angle_other_deg 3.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.088 r_dihedral_angle_3_deg 15.995 r_dihedral_angle_4_deg 13.541 r_long_range_B_refined 7.838 r_long_range_B_other 7.838 r_dihedral_angle_1_deg 7.432 r_mcangle_it 4.322 r_mcangle_other 4.321 r_scangle_other 4.284 r_angle_other_deg 3.786 r_mcbond_it 2.726 r_mcbond_other 2.726 r_scbond_it 2.657 r_scbond_other 2.655 r_angle_refined_deg 1.587 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 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 2939 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing