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Human Methionine Adenosyltransferase II mutant (R264A)
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 30% PEG600
0.1M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.141 α = 90 b = 94.23 β = 90 c = 116.82 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 PILATUS 6M 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
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 1.7 58.41 99 0.124 0.158 0.096 0.985 5.9 4.3 40576 12.4
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 1.7 1.73 99.8 0.513 0.665 0.419 0.619 4.1 4.1
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 1.7 58.41 38572 2004 98.66 0.16116 0.15997 0.1722 0.18423 0.1953 RANDOM 15.997
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] 2.85 -1.12 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.183 r_dihedral_angle_4_deg 18.731 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 6.635 r_long_range_B_refined 6.484 r_long_range_B_other 6.361 r_angle_other_deg 3.665 r_scangle_other 2.882 r_scbond_it 1.841 r_scbond_other 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.183 r_dihedral_angle_4_deg 18.731 r_dihedral_angle_3_deg 13.529 r_dihedral_angle_1_deg 6.635 r_long_range_B_refined 6.484 r_long_range_B_other 6.361 r_angle_other_deg 3.665 r_scangle_other 2.882 r_scbond_it 1.841 r_scbond_other 1.84 r_angle_refined_deg 1.695 r_mcangle_it 1.64 r_mcangle_other 1.64 r_mcbond_it 1.101 r_mcbond_other 1.097 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 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 2948 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing