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Crystal structure of recombinant chicken liver Bile Acid Binding Protein (cL-BABP) in complex with chenodeoxycholic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O0K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 281 200 mM sodium chloride, 25 % wt/vol PEG-3500 and 100 mM HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.564 α = 90 b = 60.763 β = 99.55 c = 63.546 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 EIGER2 X 16M 2023-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
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 1.65 62.67 99.2 0.046 0.049 0.019 0.999 16.4 7 32846 30.2
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 1.65 1.74 0.851 0.917 0.34 0.876 2.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.65 43.66 31255 1581 99.18 0.20536 0.2026 0.2032 0.26189 0.2601 RANDOM 38.907
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_2_deg 35.321 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_4_deg 9.973 r_long_range_B_refined 7.778 r_dihedral_angle_1_deg 7.214 r_mcangle_it 4.458 r_scbond_it 4.33 r_mcbond_it 3.22 r_angle_refined_deg 1.568 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.321 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_4_deg 9.973 r_long_range_B_refined 7.778 r_dihedral_angle_1_deg 7.214 r_mcangle_it 4.458 r_scbond_it 4.33 r_mcbond_it 3.22 r_angle_refined_deg 1.568 r_chiral_restr 0.122 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 1923 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing