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Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to orto 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 0.2M Sodium acetate trihydrate 0.1M Sodium HEPES 7.525% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 50.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.883 α = 90 b = 84.937 β = 108.399 c = 107.02 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 1.84 48.76 96.8 0.154 0.184 0.099 0.99 9.5 6.5 101754
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) 1.84 1.88 60.5 0.618 0.735 0.394 0.919 4 6.5
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 1.844 48.76 101375 5064 96.338 0.212 0.2095 0.2095 0.2593 0.2593 20.601
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] -1.085 0.903 -0.462 0.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.831 r_dihedral_angle_3_deg 13.668 r_dihedral_angle_2_deg 10.327 r_dihedral_angle_1_deg 7.961 r_lrange_it 6.382 r_scangle_it 4.385 r_scbond_it 3.321 r_mcangle_it 3.197 r_mcbond_it 2.476 r_angle_refined_deg 2.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.831 r_dihedral_angle_3_deg 13.668 r_dihedral_angle_2_deg 10.327 r_dihedral_angle_1_deg 7.961 r_lrange_it 6.382 r_scangle_it 4.385 r_scbond_it 3.321 r_mcangle_it 3.197 r_mcbond_it 2.476 r_angle_refined_deg 2.344 r_nbtor_refined 0.305 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.207 r_xyhbond_nbd_refined 0.203 r_chiral_restr 0.164 r_symmetry_xyhbond_nbd_refined 0.129 r_ncsr_local_group_1 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8420 Nucleic Acid Atoms Solvent Atoms 996 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing