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E.coli beta-galactosidase in complex with fluorescent probe KSS2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BRS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291.15 100mM Bis-Tris, pH=5.9, 200mM NaCl, 200mM MgCl2, 12% PEG8000, 5% glycerol, 3% DMSO, 3% Ethylene glycol, 10mM DTT
Crystal Properties Matthews coefficient Solvent content 2.78 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 250.658 α = 90 b = 84.953 β = 93.81 c = 243.892 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2021-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.9 44.37 99 0.218 0.235 0.088 0.981 5.6 7 112772
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 99.5 0.843 0.906 0.331 0.881 1.8 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.9 44.37 107024 5708 98.77 0.26467 0.26229 0.30942 RANDOM 63.86
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] 7.22 2.02 -5.81 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.745 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 18.564 r_long_range_B_refined 9.426 r_long_range_B_other 9.426 r_mcangle_it 7.159 r_mcangle_other 7.158 r_dihedral_angle_1_deg 7.046 r_scangle_other 6.318 r_mcbond_it 4.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.745 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 18.564 r_long_range_B_refined 9.426 r_long_range_B_other 9.426 r_mcangle_it 7.159 r_mcangle_other 7.158 r_dihedral_angle_1_deg 7.046 r_scangle_other 6.318 r_mcbond_it 4.694 r_mcbond_other 4.694 r_scbond_it 4.079 r_scbond_other 4.078 r_angle_other_deg 1.436 r_angle_refined_deg 1.2 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 31837 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing