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Structure of rsKiiro using SSX
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 8.4 295 0.2 M lithium sulfate, 0.1 M Tris-Cl, 25 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
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 99.209 0.9696252 3.884 62.2434 1633393
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 0.1295 5.6
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 1.75 54.227 24164 1215 99.649 0.174 0.1721 0.1723 0.2074 0.2077 26.752
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] 0.526 0.065 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.975 r_dihedral_angle_4_deg 21.643 r_dihedral_angle_3_deg 13.656 r_lrange_other 9.692 r_lrange_it 9.682 r_scangle_it 7.926 r_scangle_other 7.668 r_dihedral_angle_1_deg 7.055 r_scbond_it 5.345 r_scbond_other 5.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.975 r_dihedral_angle_4_deg 21.643 r_dihedral_angle_3_deg 13.656 r_lrange_other 9.692 r_lrange_it 9.682 r_scangle_it 7.926 r_scangle_other 7.668 r_dihedral_angle_1_deg 7.055 r_scbond_it 5.345 r_scbond_other 5.093 r_mcangle_it 5.085 r_mcangle_other 5.085 r_mcbond_it 3.374 r_mcbond_other 3.298 r_angle_other_deg 2.378 r_angle_refined_deg 1.704 r_symmetry_xyhbond_nbd_refined 0.37 r_nbd_refined 0.28 r_nbd_other 0.232 r_symmetry_nbd_other 0.23 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.14 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.072 r_xyhbond_nbd_other 0.054 r_bond_other_d 0.034 r_gen_planes_other 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1770 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrysalisPro data scaling REFMAC phasing