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Bile salt hydrolase from lactobacillus salivarius complex with glycocholic acid and cholic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 20% polyethylene glycol 3350, 0.2 M potassium dihydrogen phosphate pH 4.8. Then crystal is soaked in this buffer containing 5 uM glycocholic acid for 4 hrs.
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.01 α = 90 b = 94.09 β = 90.64 c = 166.974 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 RIGAKU SATURN 944 2015-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 50 95.1 0.073 12.7 5.3 143414 18.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 89.7 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 5HKE 2.1 28.5 135874 7338 94.55 0.16268 0.15994 0.1804 0.2135 0.2203 RANDOM 27.73
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] -2.19 -1.28 2.58 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.223 r_dihedral_angle_3_deg 14.208 r_dihedral_angle_4_deg 13.151 r_dihedral_angle_1_deg 6.673 r_long_range_B_refined 5.719 r_long_range_B_other 5.706 r_scangle_other 4.247 r_mcangle_it 3.374 r_mcangle_other 3.374 r_scbond_it 2.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.223 r_dihedral_angle_3_deg 14.208 r_dihedral_angle_4_deg 13.151 r_dihedral_angle_1_deg 6.673 r_long_range_B_refined 5.719 r_long_range_B_other 5.706 r_scangle_other 4.247 r_mcangle_it 3.374 r_mcangle_other 3.374 r_scbond_it 2.861 r_scbond_other 2.86 r_mcbond_it 2.309 r_mcbond_other 2.306 r_angle_refined_deg 1.682 r_angle_other_deg 1.015 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20630 Nucleic Acid Atoms Solvent Atoms 989 Heterogen Atoms 309
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing