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CysG(N-16)-H121A 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 7.5 293 0.1 M HEPES; 0.02 M MgCl2; 22% Sodium Polyacrylate 5100
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.78 α = 90 b = 49.71 β = 90.08 c = 102.51 γ = 90
Symmetry Space Group P 1 2 1
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 2023-06-03 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 1.85 30 98.3 0.094 9 2.9 85811
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 1.85 1.95 98.8 0.683 2.6 2.9
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 1.85 30 81503 4290 98.23 0.19336 0.19216 0.1998 0.23145 0.2408 RANDOM 22.328
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] 0.43 -0.78 -0.71 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.16 r_dihedral_angle_4_deg 19.426 r_dihedral_angle_3_deg 11.704 r_dihedral_angle_1_deg 6.215 r_long_range_B_refined 2.296 r_long_range_B_other 2.18 r_scangle_other 1.523 r_mcangle_it 1.355 r_mcangle_other 1.354 r_angle_other_deg 1.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.16 r_dihedral_angle_4_deg 19.426 r_dihedral_angle_3_deg 11.704 r_dihedral_angle_1_deg 6.215 r_long_range_B_refined 2.296 r_long_range_B_other 2.18 r_scangle_other 1.523 r_mcangle_it 1.355 r_mcangle_other 1.354 r_angle_other_deg 1.179 r_angle_refined_deg 1.172 r_scbond_it 1.154 r_scbond_other 1.154 r_mcbond_it 0.986 r_mcbond_other 0.986 r_rigid_bond_restr 0.539 r_chiral_restr 0.05 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 6680 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing