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CysG(N-16)-D190N mutant in complex with SAH from Kitasatospora cystarginea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FCD CysG(N-16) in complex with SAH from Kitasatospora cystarginea
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.24 M Sodium Malonate; 20% PEF 3350
Crystal Properties Matthews coefficient Solvent content 2.65 53.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.69 α = 90 b = 100.69 β = 90 c = 50.02 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 2023-04-29 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 1.4 30 99.7 0.054 15.4 5.4 50991
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 1.4 1.5 0.752 2.5
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 1.4 30 48401 2547 99.64 0.15108 0.14976 0.1503 0.17612 0.176 RANDOM 21.296
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] -0.02 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.169 r_dihedral_angle_4_deg 19.504 r_dihedral_angle_3_deg 11.28 r_dihedral_angle_1_deg 6.102 r_long_range_B_refined 2.264 r_long_range_B_other 2.095 r_scangle_other 1.664 r_scbond_it 1.345 r_scbond_other 1.345 r_angle_other_deg 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.169 r_dihedral_angle_4_deg 19.504 r_dihedral_angle_3_deg 11.28 r_dihedral_angle_1_deg 6.102 r_long_range_B_refined 2.264 r_long_range_B_other 2.095 r_scangle_other 1.664 r_scbond_it 1.345 r_scbond_other 1.345 r_angle_other_deg 1.33 r_mcangle_it 1.27 r_mcangle_other 1.27 r_angle_refined_deg 1.227 r_mcbond_it 0.977 r_mcbond_other 0.975 r_rigid_bond_restr 0.663 r_chiral_restr 0.059 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 186 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing