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AzeJ in complex with SAH from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A211W0K2-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 293 1.8 M sodium potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.55 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.5 α = 90 b = 84.15 β = 90 c = 94.34 γ = 90
Symmetry Space Group P 21 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 EIGER X 16M 2023-03-25 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 3 30 94.3 0.093 14.6 5.4 21945
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 3 3.1 97.1 0.663 4.9
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 3 30 20801 1095 94.26 0.1949 0.1925 0.1968 0.24159 0.2404 RANDOM 71.013
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] 3.36 -0.23 -3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.821 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_4_deg 13.524 r_dihedral_angle_1_deg 5.227 r_long_range_B_refined 2.637 r_long_range_B_other 2.637 r_mcangle_it 1.799 r_mcangle_other 1.799 r_scangle_other 1.557 r_mcbond_it 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.821 r_dihedral_angle_3_deg 13.613 r_dihedral_angle_4_deg 13.524 r_dihedral_angle_1_deg 5.227 r_long_range_B_refined 2.637 r_long_range_B_other 2.637 r_mcangle_it 1.799 r_mcangle_other 1.799 r_scangle_other 1.557 r_mcbond_it 1.19 r_mcbond_other 1.19 r_angle_refined_deg 1.168 r_scbond_it 1.057 r_scbond_other 1.057 r_angle_other_deg 1.032 r_rigid_bond_restr 0.19 r_chiral_restr 0.029 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 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 7108 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing