☰ Navigation Tabs
Xenorhabdin methyltransferase XrdM with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold not applicable
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 293 0.1 M Bicine pH 9.0, 30 % PEG6000
Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.5 α = 90 b = 72.5 β = 90 c = 104.96 γ = 90
Symmetry Space Group P 43 21 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-F 2022-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.1 46 99.6 0.041 18.6 5.4 16946
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 2.1 2.2 99.8 0.697 2.3 5.3
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 2.1 30 16059 845 99.66 0.20161 0.20016 0.2089 0.2289 0.2409 RANDOM 62.081
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] -0.76 -0.76 1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.017 r_dihedral_angle_4_deg 15.421 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 6.326 r_long_range_B_refined 5.678 r_long_range_B_other 5.678 r_mcangle_it 4.528 r_mcangle_other 4.528 r_scangle_other 4.058 r_mcbond_it 3.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.017 r_dihedral_angle_4_deg 15.421 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_1_deg 6.326 r_long_range_B_refined 5.678 r_long_range_B_other 5.678 r_mcangle_it 4.528 r_mcangle_other 4.528 r_scangle_other 4.058 r_mcbond_it 3.162 r_mcbond_other 3.16 r_scbond_it 3.127 r_scbond_other 3.126 r_angle_refined_deg 1.168 r_angle_other_deg 1.116 r_rigid_bond_restr 0.781 r_chiral_restr 0.043 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 1619 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing