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Crystal structure of Esub1
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, SITTING DROP 278 0.2M Lithium sulfate
0.1M Tris pH 8.5
40% PEG 400
12 mg/mL protein
Crystal Properties Matthews coefficient Solvent content 3.1 60.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.362 α = 90 b = 43.872 β = 118.668 c = 85.841 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 PILATUS 6M 2022-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.1806 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.9 43.911 99 0.08 0.043 0.999 9.9 3.4 12089
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.08 94 0.627 0.334 0.94 2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 43.911 12087 583 98.46 0.224 0.2217 0.2243 0.2806 0.282
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] -5.182 -1.009 8.04 -1.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.409 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 17.377 r_dihedral_angle_1_deg 6.563 r_lrange_it 6.034 r_lrange_other 6.027 r_scangle_it 4.114 r_scangle_other 4.113 r_mcangle_it 3.539 r_mcangle_other 3.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.409 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 17.377 r_dihedral_angle_1_deg 6.563 r_lrange_it 6.034 r_lrange_other 6.027 r_scangle_it 4.114 r_scangle_other 4.113 r_mcangle_it 3.539 r_mcangle_other 3.537 r_scbond_it 2.466 r_scbond_other 2.465 r_mcbond_it 2.264 r_mcbond_other 2.262 r_angle_refined_deg 1.814 r_angle_other_deg 1.272 r_symmetry_xyhbond_nbd_refined 0.472 r_nbd_other 0.406 r_xyhbond_nbd_other 0.373 r_symmetry_nbd_refined 0.355 r_nbd_refined 0.225 r_symmetry_nbd_other 0.206 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.172 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.07 r_ncsr_local_group_1 0.039 r_symmetry_xyhbond_nbd_other 0.021 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3124 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing