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Crystal structure of apo Zebrafish Ileal Bile Acid-Binding Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Sodium HEPES, 1.4 M tri-sodium citrate dihydrate, 1% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.422 α = 90 b = 54.422 β = 90 c = 82.696 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 315 toroidal mirror 2007-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97 ESRF ID29
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 1.6 41 99.1 0.069 0.069 16.9 5.2 18986 18986 15.8
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 1.6 1.69 100 0.281 0.281 6.4 5.3 2731
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 2QO4 1.6 30 18978 18001 977 98.66 0.20433 0.20433 0.20246 0.2029 0.2398 0.2413 RANDOM 17.547
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] 0.36 0.18 0.36 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.14 r_dihedral_angle_3_deg 14.941 r_dihedral_angle_4_deg 13.374 r_dihedral_angle_1_deg 5.381 r_scangle_it 3.253 r_scbond_it 2.088 r_mcangle_it 1.274 r_angle_refined_deg 1.155 r_mcbond_it 0.855 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.14 r_dihedral_angle_3_deg 14.941 r_dihedral_angle_4_deg 13.374 r_dihedral_angle_1_deg 5.381 r_scangle_it 3.253 r_scbond_it 2.088 r_mcangle_it 1.274 r_angle_refined_deg 1.155 r_mcbond_it 0.855 r_nbtor_refined 0.303 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1030 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling