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Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to p-hydroxybenzaldehyde
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 20% w/v Polyethyleneglycol 3,350 200mM Ammonium acetate 30% GOL
Crystal Properties Matthews coefficient Solvent content 2.27 45.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.836 α = 90 b = 83.808 β = 104.498 c = 98.117 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2024-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.87313 ESRF ID23-1
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 2 69.55 89.1 0.111 0.156 0.11 0.989 4.5 3 67761
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) 2 2.05 97.1 0.452 0.633 0.443 0.731 1.5 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 69.548 67740 3363 88.916 0.182 0.1799 0.1799 0.2181 0.2181 23.128
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] -1.511 -1.167 1.081 0.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.855 r_dihedral_angle_6_deg 13.515 r_dihedral_angle_1_deg 8.765 r_dihedral_angle_2_deg 8.73 r_lrange_it 5.596 r_scangle_it 3.729 r_scbond_it 2.418 r_mcangle_it 2.357 r_angle_refined_deg 2.193 r_mcbond_it 1.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.855 r_dihedral_angle_6_deg 13.515 r_dihedral_angle_1_deg 8.765 r_dihedral_angle_2_deg 8.73 r_lrange_it 5.596 r_scangle_it 3.729 r_scbond_it 2.418 r_mcangle_it 2.357 r_angle_refined_deg 2.193 r_mcbond_it 1.541 r_nbtor_refined 0.26 r_metal_ion_refined 0.185 r_chiral_restr 0.172 r_nbd_refined 0.134 r_symmetry_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.114 r_xyhbond_nbd_refined 0.083 r_ncsr_local_group_1 0.045 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8420 Nucleic Acid Atoms Solvent Atoms 874 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing