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Crystal structure of sulX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 24%PEG 500, 1.2 mM Zinc sulfate, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.96 68.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.236 α = 90 b = 134.236 β = 90 c = 139.84 γ = 120
Symmetry Space Group P 62 2 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 CCD RAYONIX MX-300 2023-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.03 25 98.9 1 23.27 11.3 15495
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.03 3.14 0.944 2.17
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 3.03 24.22 14119 746 94.52 0.21949 0.21562 0.2235 0.29785 0.3016 RANDOM 113.772
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] 4.02 2.01 4.02 -13.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.783 r_dihedral_angle_3_deg 19.6 r_dihedral_angle_4_deg 19.319 r_long_range_B_refined 16.827 r_long_range_B_other 16.825 r_scangle_other 14.063 r_mcangle_it 13.821 r_mcangle_other 13.821 r_mcbond_it 9.669 r_mcbond_other 9.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.783 r_dihedral_angle_3_deg 19.6 r_dihedral_angle_4_deg 19.319 r_long_range_B_refined 16.827 r_long_range_B_other 16.825 r_scangle_other 14.063 r_mcangle_it 13.821 r_mcangle_other 13.821 r_mcbond_it 9.669 r_mcbond_other 9.655 r_scbond_it 9.574 r_scbond_other 9.554 r_dihedral_angle_1_deg 8.319 r_angle_refined_deg 1.626 r_angle_other_deg 1.257 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3017 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SAINT data scaling PHASER phasing