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VioH in complex with SAH from Cystobacter Violaceus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A2S1TM86-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 293 1.4 M sodium potassium phosphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.01 α = 90 b = 77.6 β = 90 c = 84.39 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 2023-04-29 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 30 91.5 0.099 8.2 3.6 21394
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 92.7 0.54 2.8 3.5
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 20315 1069 90.36 0.20005 0.19738 0.2097 0.2494 0.2574 RANDOM 24.482
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] 0.37 -3.48 3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.468 r_dihedral_angle_4_deg 17.714 r_dihedral_angle_3_deg 14.265 r_dihedral_angle_1_deg 6.653 r_long_range_B_refined 2.245 r_long_range_B_other 2.224 r_scangle_other 1.659 r_mcangle_it 1.631 r_mcangle_other 1.631 r_angle_refined_deg 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.468 r_dihedral_angle_4_deg 17.714 r_dihedral_angle_3_deg 14.265 r_dihedral_angle_1_deg 6.653 r_long_range_B_refined 2.245 r_long_range_B_other 2.224 r_scangle_other 1.659 r_mcangle_it 1.631 r_mcangle_other 1.631 r_angle_refined_deg 1.23 r_scbond_other 1.222 r_scbond_it 1.221 r_mcbond_it 1.137 r_mcbond_other 1.137 r_angle_other_deg 1.083 r_rigid_bond_restr 0.512 r_chiral_restr 0.047 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 3722 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing