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Crystal structure of Zebrafish Ileal Bile Acid-Bindin Protein complexed with cholic acid (crystal form B).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ELZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Sodium HEPES, 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.02 69.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.285 α = 90 b = 85.285 β = 127.65 c = 75.055 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 CCD MAR CCD 165 mm Double crystal (Si111, Si220) 2006-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.03 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.2 30 98.6 0.059 0.059 9.1 3.1 24125 24125 43.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 97.3 0.312 0.312 1.3 3.1 2395
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3ELZ 2.2 30 24125 22888 1237 98.63 0.2272 0.2272 0.22566 0.224 0.25422 0.2521 RANDOM 38.977
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] 0.37 0.34 0.53 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.923 r_dihedral_angle_4_deg 23.375 r_dihedral_angle_3_deg 17.106 r_dihedral_angle_1_deg 5.476 r_scangle_it 2.16 r_angle_refined_deg 1.536 r_scbond_it 1.414 r_mcangle_it 1.003 r_mcbond_it 0.589 r_nbtor_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.923 r_dihedral_angle_4_deg 23.375 r_dihedral_angle_3_deg 17.106 r_dihedral_angle_1_deg 5.476 r_scangle_it 2.16 r_angle_refined_deg 1.536 r_scbond_it 1.414 r_mcangle_it 1.003 r_mcbond_it 0.589 r_nbtor_refined 0.33 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.158 r_symmetry_hbond_refined 0.12 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2055 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 261
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement AUTOMAR data reduction