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gamma-PSPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH and alpha-PSPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9SM3 gamma-PSPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M TRIS, 0.2 M MgCl2, 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.6 52.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.45 α = 90 b = 83.67 β = 90.64 c = 121.74 γ = 90
Symmetry Space Group C 1 2 1
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 2.6 30 97.6 0.097 7.5 3.1 32260
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 2.6 2.7 99.4 0.752 2 3.2
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 2.6 30 30634 1612 97.53 0.20943 0.20545 0.2147 0.24224 0.2455 RANDOM 63.676
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] -0.35 -1.05 -1.19 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.285 r_dihedral_angle_4_deg 21.187 r_dihedral_angle_3_deg 15.607 r_dihedral_angle_1_deg 6.459 r_long_range_B_refined 4.109 r_long_range_B_other 4.097 r_mcangle_it 1.815 r_mcangle_other 1.814 r_scangle_other 1.53 r_angle_refined_deg 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.285 r_dihedral_angle_4_deg 21.187 r_dihedral_angle_3_deg 15.607 r_dihedral_angle_1_deg 6.459 r_long_range_B_refined 4.109 r_long_range_B_other 4.097 r_mcangle_it 1.815 r_mcangle_other 1.814 r_scangle_other 1.53 r_angle_refined_deg 1.32 r_angle_other_deg 1.11 r_mcbond_it 1.024 r_mcbond_other 1.024 r_scbond_it 0.859 r_scbond_other 0.843 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6495 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing