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Structure of Orange Carotenoid Protein with canthaxanthin bound
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 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.569 α = 90 b = 82.569 β = 90 c = 87.365 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 2 1 x-ray 50 PIXEL DECTRIS PILATUS 12M 2020-07-29 M SINGLE WAVELENGTH 3 1 x-ray 50 PIXEL DECTRIS PILATUS 12M 2020-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9796 Diamond I03 2 SYNCHROTRON DIAMOND BEAMLINE I23 4.42801 Diamond I23 3 SYNCHROTRON DIAMOND BEAMLINE I23 4.27532 Diamond I23
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 1.36 87.29 99.97 0.075 0.079 0.025 17.1 19.9 74252
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.4 100 3.543 3.48 0.779 0.519 1.1 19.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XB5 1.36 55.396 74207 3699 99.884 0.19 0.189 0.189 0.2179 0.2179 RANDOM 25.954
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] 0.001 0.001 -0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.514 r_dihedral_angle_4_deg 16.814 r_dihedral_angle_3_deg 12.579 r_lrange_it 7.807 r_dihedral_angle_1_deg 5.822 r_scangle_it 4.593 r_scbond_it 3.173 r_mcangle_it 3.096 r_mcbond_it 2.152 r_angle_refined_deg 1.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.514 r_dihedral_angle_4_deg 16.814 r_dihedral_angle_3_deg 12.579 r_lrange_it 7.807 r_dihedral_angle_1_deg 5.822 r_scangle_it 4.593 r_scbond_it 3.173 r_mcangle_it 3.096 r_mcbond_it 2.152 r_angle_refined_deg 1.957 r_nbtor_refined 0.314 r_symmetry_nbd_refined 0.275 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.205 r_chiral_restr 0.117 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2376 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing SHELXCD phasing