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Structure of the StayRose dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 Structure Screen condition E9
Ethylene glycol as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.88 57.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.306 α = 90 b = 133.306 β = 90 c = 58.35 γ = 120
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 2022-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.65 43.63 98.5 0.15 0.033 0.999 14.3 20.7 70220 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 95.4 1.423 0.335 0.784 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 43.63 70210 3503 98.484 0.156 0.1544 0.1671 0.1785 0.1888 COPIED FROM 8BXT 18.368
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] 0.393 0.196 0.393 -1.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.803 r_dihedral_angle_2_deg 14.578 r_dihedral_angle_other_2_deg 14.155 r_dihedral_angle_3_deg 11.762 r_dihedral_angle_1_deg 7.382 r_lrange_it 6.069 r_lrange_other 5.949 r_scangle_it 4.918 r_scangle_other 4.917 r_scbond_it 3.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.803 r_dihedral_angle_2_deg 14.578 r_dihedral_angle_other_2_deg 14.155 r_dihedral_angle_3_deg 11.762 r_dihedral_angle_1_deg 7.382 r_lrange_it 6.069 r_lrange_other 5.949 r_scangle_it 4.918 r_scangle_other 4.917 r_scbond_it 3.229 r_scbond_other 3.228 r_mcangle_it 2.7 r_mcangle_other 2.7 r_mcbond_it 1.83 r_mcbond_other 1.83 r_angle_refined_deg 1.808 r_angle_other_deg 0.644 r_nbd_other 0.24 r_symmetry_nbd_other 0.204 r_nbd_refined 0.198 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.172 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.095 r_symmetry_xyhbond_nbd_other 0.029 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3459 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing