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Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FTB PDB ENTRY 2FTB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 293 1.6M sodium citrate, 0.1M hepes, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.03 59.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.664 α = 90 b = 73.664 β = 90 c = 61.546 γ = 90
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 4 2005-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 47.25 96.2 0.065 5508
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.56 99.5 0.14
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 2FTB 2.5 30 5249 5249 252 95.26 0.26013 0.26013 0.25756 0.2539 0.31598 0.3151 RANDOM 49.5
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] -1.2 -1.2 2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.09 r_dihedral_angle_3_deg 18.83 r_dihedral_angle_4_deg 18.367 r_dihedral_angle_1_deg 5.304 r_angle_refined_deg 1.223 r_scangle_it 1.084 r_scbond_it 0.639 r_mcangle_it 0.595 r_mcbond_it 0.336 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.09 r_dihedral_angle_3_deg 18.83 r_dihedral_angle_4_deg 18.367 r_dihedral_angle_1_deg 5.304 r_angle_refined_deg 1.223 r_scangle_it 1.084 r_scbond_it 0.639 r_mcangle_it 0.595 r_mcbond_it 0.336 r_nbtor_refined 0.32 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.088 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 966 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing