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Structure of rsKiiro using SSX after illumination with 0.53 mJ/mm^2 of 405 nm light
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.4 290 0.2 M lithium sulfate, 0.1 M Tris-Cl, 25 % PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.6 α = 90 b = 74.5 β = 90 c = 78.9 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 290 PIXEL DECTRIS EIGER X 4M 2019-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9801 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.7 78.69 98.7902 0.971 3.556 50.2697 1313598
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 1.7 1.761 0.004941 4.5
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 1.7 54.227 26057 1284 98.723 0.19 0.1904 0.1905 0.1916 0.1926 24.769
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] 0.571 -0.162 -0.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.537 r_dihedral_angle_4_deg 18.134 r_dihedral_angle_3_deg 13.874 r_lrange_it 8.884 r_lrange_other 8.725 r_dihedral_angle_1_deg 7.715 r_scangle_it 3.547 r_scangle_other 3.542 r_mcangle_it 2.825 r_mcangle_other 2.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.537 r_dihedral_angle_4_deg 18.134 r_dihedral_angle_3_deg 13.874 r_lrange_it 8.884 r_lrange_other 8.725 r_dihedral_angle_1_deg 7.715 r_scangle_it 3.547 r_scangle_other 3.542 r_mcangle_it 2.825 r_mcangle_other 2.824 r_angle_other_deg 2.354 r_scbond_it 2.169 r_scbond_other 2.165 r_mcbond_it 1.664 r_mcbond_other 1.662 r_angle_refined_deg 1.507 r_xyhbond_nbd_other 0.267 r_nbd_refined 0.255 r_symmetry_xyhbond_nbd_refined 0.229 r_xyhbond_nbd_refined 0.224 r_symmetry_nbd_other 0.223 r_nbd_other 0.192 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.151 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.06 r_symmetry_xyhbond_nbd_other 0.05 r_bond_other_d 0.035 r_gen_planes_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3508 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling REFMAC phasing