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gamma-PSPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M BIS-TRIS, 1.5 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.62 53.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.22 α = 89.88 b = 68.32 β = 89.52 c = 120.68 γ = 76.31
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 EIGER X 16M 2024-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.05 30 93.9 0.092 8.4 2.8 124759
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.15 95.8 0.727 2 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.05 30 118495 6236 93.89 0.17986 0.17788 0.1843 0.21431 0.2246 RANDOM 36.533
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] -1.8 0.06 0.99 -0.58 -1 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.05 r_dihedral_angle_4_deg 19.786 r_dihedral_angle_3_deg 13.62 r_dihedral_angle_1_deg 6.565 r_long_range_B_refined 3.841 r_long_range_B_other 3.825 r_mcangle_it 2.76 r_mcangle_other 2.76 r_scangle_other 2.656 r_scbond_it 1.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.05 r_dihedral_angle_4_deg 19.786 r_dihedral_angle_3_deg 13.62 r_dihedral_angle_1_deg 6.565 r_long_range_B_refined 3.841 r_long_range_B_other 3.825 r_mcangle_it 2.76 r_mcangle_other 2.76 r_scangle_other 2.656 r_scbond_it 1.956 r_scbond_other 1.949 r_mcbond_it 1.946 r_mcbond_other 1.946 r_angle_refined_deg 1.22 r_angle_other_deg 1.135 r_rigid_bond_restr 0.615 r_chiral_restr 0.051 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13624 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing