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bile salt hydrolase from Lactobacillus salivarius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 20% Polyethylene glycol 3350, 0.2M potassium dihydrogen phosphate pH 4.8
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.79 α = 90 b = 87.356 β = 90 c = 86.766 γ = 90
Symmetry Space Group P 21 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 100 CCD RIGAKU SATURN 944 2015-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 1.9 50 99.3 0.054 28.9 5.7 54757 13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 90 0.236 4.91 3.6
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 2bjf 1.9 45.5 52091 2619 99.19 0.15315 0.15155 0.1646 0.18533 0.1959 RANDOM 19.805
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] -0.22 0.77 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.692 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_4_deg 11.993 r_dihedral_angle_1_deg 6.474 r_long_range_B_refined 5.931 r_long_range_B_other 5.914 r_scangle_other 4.887 r_scbond_it 3.289 r_scbond_other 3.252 r_mcangle_it 2.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.692 r_dihedral_angle_3_deg 12.711 r_dihedral_angle_4_deg 11.993 r_dihedral_angle_1_deg 6.474 r_long_range_B_refined 5.931 r_long_range_B_other 5.914 r_scangle_other 4.887 r_scbond_it 3.289 r_scbond_other 3.252 r_mcangle_it 2.326 r_mcangle_other 2.326 r_angle_refined_deg 1.877 r_mcbond_it 1.826 r_mcbond_other 1.808 r_angle_other_deg 1.391 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.008 r_gen_planes_other 0.006 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 5058 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing