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CysG(N-16) in complex with SAH from Kitasatospora cystarginea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A1W6R556-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2.0 M (NH4)2SO4; 0.1 M HEPES; 2% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.66 53.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.19 α = 90 b = 101.19 β = 90 c = 49.79 γ = 90
Symmetry Space Group P 4 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 1.5 30 96 0.057 15.3 4.5 40256
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 1.5 1.6 96.4 0.642 3.5 4.6
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 1.5 30 38239 2012 95.97 0.14721 0.14594 0.1445 0.17149 0.1707 RANDOM 20.024
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] -0.88 -0.88 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.145 r_dihedral_angle_4_deg 23.316 r_dihedral_angle_3_deg 12.368 r_dihedral_angle_1_deg 5.921 r_long_range_B_refined 2.874 r_long_range_B_other 2.801 r_scangle_other 2.128 r_mcangle_it 1.8 r_mcangle_other 1.799 r_scbond_it 1.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.145 r_dihedral_angle_4_deg 23.316 r_dihedral_angle_3_deg 12.368 r_dihedral_angle_1_deg 5.921 r_long_range_B_refined 2.874 r_long_range_B_other 2.801 r_scangle_other 2.128 r_mcangle_it 1.8 r_mcangle_other 1.799 r_scbond_it 1.705 r_scbond_other 1.704 r_angle_other_deg 1.344 r_mcbond_it 1.296 r_mcbond_other 1.293 r_angle_refined_deg 1.226 r_rigid_bond_restr 0.903 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 1675 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing