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The structure of Human Methionine Adenosyltransferase II in apo state
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 35% PEG600
0.1M HEPES pH7.0
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.176 α = 90 b = 103.232 β = 90 c = 108.359 γ = 90
Symmetry Space Group P 2 21 21
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 PILATUS 6M 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.98 Diamond I24
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 1.95 74.74 99.6 0.181 0.236 0.15 0.94 4.7 3.5 51446 9.937
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 1.95 2 99.8 0.387 0.506 0.322 0.845 2.1 3.6
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 5A1I 1.95 74.74 48711 2690 99.62 0.19146 0.18964 0.1975 0.22387 0.2302 RANDOM 14.511
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] 2.96 -1.72 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.257 r_dihedral_angle_4_deg 16.17 r_dihedral_angle_3_deg 13.792 r_dihedral_angle_1_deg 6.408 r_long_range_B_refined 3.955 r_long_range_B_other 3.954 r_angle_other_deg 3.737 r_scangle_other 2.257 r_mcangle_it 1.837 r_mcangle_other 1.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.257 r_dihedral_angle_4_deg 16.17 r_dihedral_angle_3_deg 13.792 r_dihedral_angle_1_deg 6.408 r_long_range_B_refined 3.955 r_long_range_B_other 3.954 r_angle_other_deg 3.737 r_scangle_other 2.257 r_mcangle_it 1.837 r_mcangle_other 1.836 r_angle_refined_deg 1.666 r_scbond_it 1.368 r_scbond_other 1.366 r_mcbond_it 1.066 r_mcbond_other 1.065 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 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 5711 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing