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Cis structure intermediate of rsKiiro Illuminated at 200 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OOZ experimental model PDB 5OQA
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 2.25 45.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.648 α = 90 b = 73.746 β = 90 c = 78.142 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 100 PIXEL DECTRIS PILATUS3 6M 2018-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.7293 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.458 53.691 87 0.135 0.999 10.7 13.1 34516
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 1.459 1.546 0.643 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5OOZ, 5OQA 1.458 53.691 34516 1672 86.735 0.173 0.1717 0.1717 0.1973 0.1972 18.663
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] 0.009 0.012 -0.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.092 r_dihedral_angle_4_deg 22.773 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 7.458 r_lrange_it 5.967 r_lrange_other 5.76 r_scangle_it 4.148 r_scangle_other 4.139 r_scbond_it 2.711 r_scbond_other 2.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.092 r_dihedral_angle_4_deg 22.773 r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 7.458 r_lrange_it 5.967 r_lrange_other 5.76 r_scangle_it 4.148 r_scangle_other 4.139 r_scbond_it 2.711 r_scbond_other 2.682 r_mcangle_other 2.42 r_mcangle_it 2.418 r_angle_refined_deg 1.834 r_mcbond_it 1.693 r_mcbond_other 1.689 r_angle_other_deg 1.467 r_symmetry_xyhbond_nbd_refined 0.374 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.202 r_nbd_other 0.184 r_nbtor_refined 0.174 r_symmetry_nbd_refined 0.128 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 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 1747 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling REFMAC phasing