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Crystal structure of OcuKAI2d2 from Orobanche cumana bound to Dehydrocostus Lactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 3.15 61.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.84 α = 90 b = 150.84 β = 90 c = 57.6 γ = 120
Symmetry Space Group P 64 2 2
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 9M 2019-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.987 SOLEIL PROXIMA 2
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 2.45 49.13 99.9 0.75 19 20 14697
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 98.8 0.534 0.9
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.45 45.82 14697 989 99.91 0.1868 0.2202 0.2372 0.2535 RANDOM 49.213
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] 0.29 0.15 0.29 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.254 r_dihedral_angle_1_deg 7.25 r_scangle_it 3.773 r_scangle_other 3.638 r_mcangle_it 3.386 r_mcangle_other 3.386 r_scbond_it 2.33 r_scbond_other 2.234 r_mcbond_it 2.13 r_mcbond_other 2.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.254 r_dihedral_angle_1_deg 7.25 r_scangle_it 3.773 r_scangle_other 3.638 r_mcangle_it 3.386 r_mcangle_other 3.386 r_scbond_it 2.33 r_scbond_other 2.234 r_mcbond_it 2.13 r_mcbond_other 2.129 r_angle_refined_deg 1.689 r_angle_other_deg 1.524 r_nbd_refined 0.234 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.173 r_nbd_other 0.16 r_chiral_restr 0.064 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_other 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_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2115 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing