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Crystal structure of the carotenoid isomerooxygenase, NinaB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A8Y9I2-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 40% (v/v) MPD
100 mM sodium cacodylate, pH 6.5
5% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 349.934 α = 90 b = 52.036 β = 98.95 c = 210.036 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2021-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 50 98.6 0.152 0.996 5.6 3.9 271195
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 1.95 2.07 95.7 1.401 0.435 0.92
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.95 49.67 257803 13352 98.56 0.21891 0.21747 0.24677 0.2419 RANDOM 36.073
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] -0.89 -0.21 3.1 -2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 14.824 r_dihedral_angle_3_deg 12.467 r_dihedral_angle_1_deg 7.047 r_long_range_B_refined 4.863 r_long_range_B_other 4.86 r_scangle_other 2.876 r_mcangle_it 2.62 r_mcangle_other 2.62 r_scbond_it 1.717 r_scbond_other 1.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 14.824 r_dihedral_angle_3_deg 12.467 r_dihedral_angle_1_deg 7.047 r_long_range_B_refined 4.863 r_long_range_B_other 4.86 r_scangle_other 2.876 r_mcangle_it 2.62 r_mcangle_other 2.62 r_scbond_it 1.717 r_scbond_other 1.717 r_mcbond_it 1.588 r_mcbond_other 1.587 r_angle_refined_deg 0.844 r_dihedral_angle_2_deg 0.748 r_angle_other_deg 0.296 r_chiral_restr 0.042 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31357 Nucleic Acid Atoms Solvent Atoms 2071 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing