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Crystal structure of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7 in space group C2221
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1 M CAPS (pH 10.5), 0.2 M lithium sulfate and 2 M ammonium sulfate using in situ proteolysis (1:1000 (w/w) ratio of trypsin:protein
Crystal Properties Matthews coefficient Solvent content 2.91 57.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.975 α = 90 b = 376.119 β = 90 c = 109.487 γ = 90
Symmetry Space Group C 2 2 21
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 2M 2014-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.459 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.15 50 99 0.086 0.103 8.19 3.1 123301 -3 42.751
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.28 96 0.756 0.965 1.17
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 4PTV 2.15 20 123301 6550 99.52 0.189 0.1875 0.1966 0.2175 0.2256 RANDOM 44.182
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] -0.79 -0.62 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.302 r_dihedral_angle_4_deg 18.044 r_dihedral_angle_3_deg 12.921 r_dihedral_angle_1_deg 6.562 r_mcangle_it 2.34 r_mcbond_it 1.545 r_mcbond_other 1.545 r_angle_refined_deg 1.36 r_angle_other_deg 0.955 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.302 r_dihedral_angle_4_deg 18.044 r_dihedral_angle_3_deg 12.921 r_dihedral_angle_1_deg 6.562 r_mcangle_it 2.34 r_mcbond_it 1.545 r_mcbond_other 1.545 r_angle_refined_deg 1.36 r_angle_other_deg 0.955 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14456 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 121
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing