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Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to oleic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TVQ PDB ENTRY 1TVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 30% PEG 4000, 0.2M sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.434 α = 90 b = 66.434 β = 90 c = 61.724 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE RIGAKU RAXIS II graphite crystal monochromator 2000-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 45 99.9 0.041 9823 9823
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 2.05 100 0.185
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 1TVQ 2 20 9318 9318 469 99.87 0.21755 0.21755 0.21544 0.2157 0.26197 0.2593 RANDOM 23.801
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] -0.18 -0.18 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.57 r_dihedral_angle_3_deg 15.912 r_dihedral_angle_4_deg 9.614 r_dihedral_angle_1_deg 5.981 r_scangle_it 2.465 r_scbond_it 1.526 r_mcangle_it 1.267 r_angle_refined_deg 1.128 r_mcbond_it 0.747 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.57 r_dihedral_angle_3_deg 15.912 r_dihedral_angle_4_deg 9.614 r_dihedral_angle_1_deg 5.981 r_scangle_it 2.465 r_scbond_it 1.526 r_mcangle_it 1.267 r_angle_refined_deg 1.128 r_mcbond_it 0.747 r_nbtor_refined 0.294 r_nbd_refined 0.174 r_symmetry_hbond_refined 0.144 r_symmetry_vdw_refined 0.131 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.068 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 37 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing