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AzeJ in complex with MTA and AZE from Pseudomonas aeruginosa (P2(1)2(1)2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RYD AzeJ in complex with SAH from Pseudomonas aeruginosa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M HEPES, 2.4 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.64 α = 90 b = 82.15 β = 90 c = 94.67 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 1.95 30 98.1 0.058 16.3 4.5 80170
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 1.95 2.05 98.7 0.688
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 1.95 30 76143 4008 98.07 0.16625 0.164 0.1759 0.20921 0.2176 RANDOM 37.695
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] -1.3 0.44 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.138 r_dihedral_angle_4_deg 15.638 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_1_deg 6.784 r_long_range_B_refined 4.284 r_long_range_B_other 4.243 r_scangle_other 3.355 r_mcangle_other 3.046 r_mcangle_it 3.045 r_scbond_it 2.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.138 r_dihedral_angle_4_deg 15.638 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_1_deg 6.784 r_long_range_B_refined 4.284 r_long_range_B_other 4.243 r_scangle_other 3.355 r_mcangle_other 3.046 r_mcangle_it 3.045 r_scbond_it 2.563 r_scbond_other 2.563 r_mcbond_it 2.188 r_mcbond_other 2.185 r_angle_refined_deg 1.227 r_angle_other_deg 1.207 r_rigid_bond_restr 0.749 r_chiral_restr 0.049 r_bond_refined_d 0.004 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 7344 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing