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Crystal structure of the glycine 55 arginine mutant 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 2QO4
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 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.496 α = 90 b = 43.496 β = 90 c = 67.348 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 IMAGE PLATE MAR scanner 345 mm plate toroidal mirror 2005-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.87 50 98.3 0.072 0.072 6.6 3.5 11016 11016 25.9
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 1.87 1.94 92.1 0.327 0.327 1.7 3.3 960
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 FOURIER SYNTHESIS THROUGHOUT 2QO4 1.9 25 9964 9964 495 93.17 0.20657 0.20657 0.20472 0.2042 0.24458 0.2406 RANDOM 17.598
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] 0.17 0.08 0.17 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.137 r_dihedral_angle_3_deg 13.297 r_dihedral_angle_4_deg 7.995 r_dihedral_angle_1_deg 5.898 r_scangle_it 2.31 r_scbond_it 1.447 r_angle_refined_deg 1.28 r_mcangle_it 0.84 r_mcbond_it 0.532 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.137 r_dihedral_angle_3_deg 13.297 r_dihedral_angle_4_deg 7.995 r_dihedral_angle_1_deg 5.898 r_scangle_it 2.31 r_scbond_it 1.447 r_angle_refined_deg 1.28 r_mcangle_it 0.84 r_mcbond_it 0.532 r_nbtor_refined 0.307 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.135 r_symmetry_hbond_refined 0.122 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 979 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection AUTOMAR data reduction