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Structure of a GH3 b-glucosidase from cow rumen metagenome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 25% PEG 3350, 0.1M Na malonate pH 7.0, then soaked in 25% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.76 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.215 α = 90 b = 119.724 β = 90 c = 157.489 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 100 PIXEL DECTRIS PILATUS 6M 2014-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.83 95.31 98.9 0.137 0.994 8.7 6.4 84644
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 1.83 1.87 87.2 0.562 2.1 5.6
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 2x42 1.83 95.31 80259 4317 98.78 0.15789 0.15676 0.1671 0.17854 0.1845 RANDOM 20.032
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] 0.3 -0.62 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.972 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_3_deg 11.126 r_dihedral_angle_1_deg 6.124 r_long_range_B_refined 4.305 r_long_range_B_other 3.892 r_scangle_other 1.953 r_mcangle_it 1.426 r_mcangle_other 1.426 r_angle_refined_deg 1.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.972 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_3_deg 11.126 r_dihedral_angle_1_deg 6.124 r_long_range_B_refined 4.305 r_long_range_B_other 3.892 r_scangle_other 1.953 r_mcangle_it 1.426 r_mcangle_other 1.426 r_angle_refined_deg 1.209 r_scbond_it 1.186 r_scbond_other 1.185 r_angle_other_deg 0.891 r_mcbond_it 0.843 r_mcbond_other 0.839 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6142 Nucleic Acid Atoms Solvent Atoms 674 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing