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Crystal structure of the cysteine 91 threonine 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 PDB ENTRY 2QO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.2M ammonium acetate, 30% PEG 4000, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.13 42.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.012 α = 90 b = 63.276 β = 105.51 c = 35.671 γ = 90
Symmetry Space Group P 1 21 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 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 21.1 99.4 0.065 0.065 16.8 3.6 19136 19136 12.1
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) 1.5 1.58 100 0.133 0.133 8.2 3.6 2791
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 2QO4 1.5 25 18134 18134 982 99.39 0.22015 0.22015 0.2186 0.2161 0.24893 0.2471 RANDOM 12.049
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] 0.31 0.46 -0.56 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.488 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 13.418 r_dihedral_angle_1_deg 5.456 r_scangle_it 2.161 r_scbond_it 1.357 r_angle_refined_deg 1.217 r_mcangle_it 0.919 r_mcbond_it 0.547 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.488 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 13.418 r_dihedral_angle_1_deg 5.456 r_scangle_it 2.161 r_scbond_it 1.357 r_angle_refined_deg 1.217 r_mcangle_it 0.919 r_mcbond_it 0.547 r_nbtor_refined 0.314 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.153 r_chiral_restr 0.076 r_xyhbond_nbd_refined 0.075 r_symmetry_hbond_refined 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 1001 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing