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Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to vanillin
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 0.1MPCTP 7.0 25% w/v PEG 1500 30% GOL
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.68 α = 90 b = 84.676 β = 108.349 c = 106.571 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 2023-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03322 PETRA III, DESY P11
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 1.67 48.56 98.8 0.087 0.103 0.054 0.999 12.6 6.9 137992
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) 1.67 1.7 98.4 1.473 1.737 0.911 0.528 1.2 7
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 1.671 48.56 137923 6946 98.667 0.164 0.1629 0.1628 0.1944 0.1945 26.999
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] -0.636 0.811 0.514 -0.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.962 r_dihedral_angle_3_deg 12.521 r_dihedral_angle_2_deg 8.176 r_dihedral_angle_1_deg 7.502 r_lrange_it 5.765 r_scangle_it 4.877 r_scbond_it 3.53 r_mcangle_it 3.01 r_mcbond_it 2.266 r_angle_refined_deg 1.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.962 r_dihedral_angle_3_deg 12.521 r_dihedral_angle_2_deg 8.176 r_dihedral_angle_1_deg 7.502 r_lrange_it 5.765 r_scangle_it 4.877 r_scbond_it 3.53 r_mcangle_it 3.01 r_mcbond_it 2.266 r_angle_refined_deg 1.919 r_symmetry_xyhbond_nbd_refined 0.324 r_nbtor_refined 0.306 r_symmetry_nbd_refined 0.194 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.124 r_ncsr_local_group_1 0.062 r_gen_planes_refined 0.011 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8406 Nucleic Acid Atoms Solvent Atoms 893 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing