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Metagenomic Beta-galactosidase from Glycoside Hydrolase family GH154
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 16% (w/v) PEG 3350, 100 mM HEPES-NaOH, pH 7.5, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.52 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.316 α = 90 b = 94.581 β = 105.45 c = 108.264 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 PIXEL DECTRIS EIGER2 S 16M 2022-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.76 47.4 96 0.987 6.1 2.53 177698
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79 56.1 0.66 0.8
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.76 47.4 168936 8761 96.09 0.15325 0.15231 0.1711 0.1989 RANDOM 33.838
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] -0.96 0.84 -0.72 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.784 r_long_range_B_refined 6.826 r_long_range_B_other 6.813 r_dihedral_angle_1_deg 5.859 r_scangle_other 5.391 r_scbond_it 3.787 r_scbond_other 3.787 r_mcangle_it 3.027 r_mcangle_other 3.027 r_mcbond_it 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.784 r_long_range_B_refined 6.826 r_long_range_B_other 6.813 r_dihedral_angle_1_deg 5.859 r_scangle_other 5.391 r_scbond_it 3.787 r_scbond_other 3.787 r_mcangle_it 3.027 r_mcangle_other 3.027 r_mcbond_it 2.27 r_mcbond_other 2.269 r_angle_refined_deg 1.264 r_angle_other_deg 0.513 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12739 Nucleic Acid Atoms Solvent Atoms 877 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing