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Carotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NPE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 Tris pH 7.5, (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 6.31 80.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.242 α = 90 b = 210.242 β = 90 c = 210.242 γ = 90
Symmetry Space Group P 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98.15 PIXEL DECTRIS EIGER X 16M 2021-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95365 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 48.3 99.98 0.999 17.5 3.6 70655
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.35 100 1.2 0.429
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 48.279 70551 3143 99.977 0.192 0.1911 0.1911 0.2093 0.2093 RANDOM 47.863
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.798 r_dihedral_angle_6_deg 17.71 r_dihedral_angle_1_deg 7.094 r_lrange_it 6.557 r_lrange_other 6.557 r_scangle_other 5.688 r_scangle_it 5.636 r_scbond_it 3.965 r_scbond_other 3.964 r_dihedral_angle_2_deg 3.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.798 r_dihedral_angle_6_deg 17.71 r_dihedral_angle_1_deg 7.094 r_lrange_it 6.557 r_lrange_other 6.557 r_scangle_other 5.688 r_scangle_it 5.636 r_scbond_it 3.965 r_scbond_other 3.964 r_dihedral_angle_2_deg 3.891 r_mcangle_it 3.769 r_mcangle_other 3.768 r_mcbond_it 2.405 r_mcbond_other 2.405 r_angle_refined_deg 1.447 r_angle_other_deg 0.745 r_symmetry_nbd_other 0.221 r_nbd_refined 0.207 r_nbd_other 0.198 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.151 r_xyhbond_nbd_refined 0.133 r_symmetry_nbd_refined 0.125 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4261 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing