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Structure of Orange Carotenoid Protein with canthaxanthin bound after 1 minute of illumination
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 100 mM sodium acetate pH 4.5, 10 %
poly-ethylene glycol 20,000, 3 % glycerol
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.58 α = 90 b = 82.58 β = 90 c = 87.22 γ = 120
Symmetry Space Group P 32 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 EIGER2 XE 16M 2019-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.32 71.49 100 0.049 0.051 0.016 23.8 18.7 80954
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.39 100 2.448 2.661 1.02 1.2 12.9
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 THROUGHOUT 4XB5 1.39 55.364 69455 3445 99.927 0.194 0.194 0.1938 0.197 0.2026 28.063
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] 0.012 0.006 0.012 -0.038
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.158 r_dihedral_angle_4_deg 20.059 r_dihedral_angle_3_deg 14.082 r_lrange_it 7.346 r_dihedral_angle_1_deg 6.839 r_scangle_it 4.005 r_mcangle_it 3.071 r_scbond_it 2.692 r_angle_refined_deg 2.325 r_mcbond_it 2.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.158 r_dihedral_angle_4_deg 20.059 r_dihedral_angle_3_deg 14.082 r_lrange_it 7.346 r_dihedral_angle_1_deg 6.839 r_scangle_it 4.005 r_mcangle_it 3.071 r_scbond_it 2.692 r_angle_refined_deg 2.325 r_mcbond_it 2.012 r_symmetry_xyhbond_nbd_refined 0.357 r_nbtor_refined 0.314 r_xyhbond_nbd_refined 0.276 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.216 r_chiral_restr 0.149 r_bond_refined_d 0.025 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2411 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing