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Crystal structure of the E25A mutant of the Orange Carotenoid Protein X from Gloeobacter kilaueensis JS1 complexed with echinenone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v Polyethylene glycol monomethyl ether 5000
Crystal Properties Matthews coefficient Solvent content 2.34 47.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.735 α = 90 b = 61.366 β = 90 c = 145.075 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 EIGER X 4M 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.73 72.54 97.9 0.088 0.102 0.049 0.994 10.3 4.1 35299
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 1.73 1.76 92.7 0.361 0.425 0.216 0.839 3.7
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 (Observed) 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 Alphafold 1.73 72.54 33412 1799 97.42 0.1595 0.1577 0.1705 0.1929 0.2018 RANDOM 14.25
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] -0.71 -0.07 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.981 r_dihedral_angle_2_deg 12.323 r_dihedral_angle_1_deg 6.61 r_angle_refined_deg 2.084 r_angle_other_deg 0.771 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2479 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 51
Software Software Software Name Purpose Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction