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Structure of Orange Carotenoid Protein with canthaxanthin bound after 10 minutes 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 2.47 50.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.26 α = 90 b = 82.26 β = 90 c = 86.25 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 2019-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9795 Diamond I03
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 1.37 29.86 100 0.046 0.048 0.015 24.6 19.2 71802
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 1.37 1.41 2.561 2.74 0.966
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 1.41 28.767 65306 3207 99.884 0.193 0.1908 0.1908 0.2301 0.2301 31.033
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] 0.068 0.034 0.068 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.192 r_dihedral_angle_4_deg 18.319 r_dihedral_angle_3_deg 13.493 r_lrange_it 7.545 r_dihedral_angle_1_deg 6.883 r_scangle_it 3.987 r_mcangle_it 3.092 r_scbond_it 2.847 r_mcbond_it 2.13 r_angle_refined_deg 1.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.192 r_dihedral_angle_4_deg 18.319 r_dihedral_angle_3_deg 13.493 r_lrange_it 7.545 r_dihedral_angle_1_deg 6.883 r_scangle_it 3.987 r_mcangle_it 3.092 r_scbond_it 2.847 r_mcbond_it 2.13 r_angle_refined_deg 1.767 r_nbtor_refined 0.317 r_symmetry_xyhbond_nbd_refined 0.291 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.214 r_symmetry_nbd_refined 0.207 r_chiral_restr 0.098 r_gen_planes_refined 0.012 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2411 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing