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beta-glucosidase GH1-family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z1H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG4000, 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.603 α = 90 b = 96.871 β = 90 c = 143.005 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 PIXEL DECTRIS EIGER X 9M 2022-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.1 PAL/PLS 5C (4A)
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 1.9 50 95.6 0.996 22.05 11.4 142431 17.11
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 1.9 1.93 0.946
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6Z1H 1.9 37.11 1.38 142431 3538 90.3 0.1556 0.155 0.1551 0.1803 0.1803 20.58
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.9112 f_angle_d 0.9669 f_chiral_restr 0.0665 f_plane_restr 0.0079 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7540 Nucleic Acid Atoms Solvent Atoms 960 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing