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Crystal structure of zebrafish liver bile acid-binding protein complexed with cholic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TW4 PDB ENTRY 1TW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 20% PEG 4000, 20% isopropanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.61 52.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.355 α = 90 b = 43.355 β = 90 c = 67.526 γ = 120
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 2005-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.98 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 1.5 33.8 94.3 0.072 0.072 13.8 2.8 21471 21471 10.6
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 1.5 1.58 72.6 0.083 0.083 6.3 1.9 2397
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 PDB ENTRY 1TW4 1.5 25 20338 20338 1104 94.34 0.18757 0.18757 0.18641 0.1859 0.20883 0.2069 RANDOM 10.209
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] -0.1 -0.05 -0.1 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.435 r_dihedral_angle_3_deg 11.245 r_dihedral_angle_4_deg 5.542 r_dihedral_angle_1_deg 5.488 r_scangle_it 2.214 r_scbond_it 1.38 r_angle_refined_deg 1.183 r_mcangle_it 0.782 r_mcbond_it 0.494 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.435 r_dihedral_angle_3_deg 11.245 r_dihedral_angle_4_deg 5.542 r_dihedral_angle_1_deg 5.488 r_scangle_it 2.214 r_scbond_it 1.38 r_angle_refined_deg 1.183 r_mcangle_it 0.782 r_mcbond_it 0.494 r_nbtor_refined 0.309 r_nbd_refined 0.174 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.084 r_chiral_restr 0.073 r_symmetry_hbond_refined 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 972 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing