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Human Methionine Adenosyltransferase II mutant (S114A) in P22121 crystal form
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
Crystal Properties Matthews coefficient Solvent content 2.08 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.09 α = 90 b = 102.871 β = 90 c = 108.17 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 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9 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 1.65 54.08 97.7 0.108 0.128 0.068 0.995 8 5.3 81704 14.9
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 1.65 1.68 98.4 0.566 0.681 0.372 0.685 1.9 5.3
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 1.65 54.08 77575 4092 97.2 0.16467 0.16316 0.1727 0.19456 0.2035 RANDOM 19.747
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] 2.28 -0.84 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.232 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 13.496 r_dihedral_angle_1_deg 6.403 r_long_range_B_refined 5.819 r_long_range_B_other 5.819 r_scangle_other 3.707 r_scbond_it 2.393 r_scbond_other 2.392 r_mcangle_it 2.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.232 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 13.496 r_dihedral_angle_1_deg 6.403 r_long_range_B_refined 5.819 r_long_range_B_other 5.819 r_scangle_other 3.707 r_scbond_it 2.393 r_scbond_other 2.392 r_mcangle_it 2.203 r_mcangle_other 2.203 r_angle_refined_deg 1.76 r_mcbond_it 1.482 r_mcbond_other 1.482 r_angle_other_deg 1.034 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 5855 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing