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CysG(N-16) in complex with SAM 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 7.1 293 0.1 M HEPES, 0.2 M NaCl, 26% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.54 α = 90 b = 101.54 β = 90 c = 49.86 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 2023-06-03 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 1.75 30 99.4 0.066 13.1 4.9 26735
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 1.75 1.85 99.8 0.781 2.3
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 1.75 30 25391 1336 99.41 0.15917 0.15703 0.1704 0.19884 0.2073 RANDOM 31.999
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] 0.79 0.79 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 16.075 r_dihedral_angle_3_deg 12.034 r_dihedral_angle_1_deg 6.357 r_long_range_B_refined 3.636 r_long_range_B_other 3.584 r_scangle_other 3.28 r_scbond_other 2.761 r_scbond_it 2.759 r_mcangle_it 2.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.705 r_dihedral_angle_4_deg 16.075 r_dihedral_angle_3_deg 12.034 r_dihedral_angle_1_deg 6.357 r_long_range_B_refined 3.636 r_long_range_B_other 3.584 r_scangle_other 3.28 r_scbond_other 2.761 r_scbond_it 2.759 r_mcangle_it 2.475 r_mcangle_other 2.474 r_mcbond_it 1.98 r_mcbond_other 1.978 r_angle_other_deg 1.232 r_angle_refined_deg 1.201 r_rigid_bond_restr 1.012 r_chiral_restr 0.054 r_bond_refined_d 0.004 r_gen_planes_refined 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 1668 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing