☰ Navigation Tabs
Structure of a GH3 b-glucosidase from cow rumen metagenome in complex with galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K6L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, then soaked in 100mM galactose.
Crystal Properties Matthews coefficient Solvent content 2.73 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.924 α = 90 b = 119.251 β = 90 c = 157.479 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 PILATUS3 6M 2016-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.1271 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.29 95.08 100 0.09 11.4 6.5 44188
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 2.29 2.37 100 0.528 3.3 6.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5K6L 2.29 95.07 41959 2150 99.94 0.18358 0.18134 0.22717 0.221 RANDOM 47.334
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] 11.74 -6.58 -5.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.333 r_dihedral_angle_4_deg 14.592 r_dihedral_angle_3_deg 14.421 r_long_range_B_other 7.025 r_long_range_B_refined 7.024 r_dihedral_angle_1_deg 6.209 r_scangle_other 5.416 r_mcangle_it 4.067 r_mcangle_other 4.066 r_scbond_it 3.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.333 r_dihedral_angle_4_deg 14.592 r_dihedral_angle_3_deg 14.421 r_long_range_B_other 7.025 r_long_range_B_refined 7.024 r_dihedral_angle_1_deg 6.209 r_scangle_other 5.416 r_mcangle_it 4.067 r_mcangle_other 4.066 r_scbond_it 3.348 r_scbond_other 3.345 r_mcbond_it 2.583 r_mcbond_other 2.58 r_angle_refined_deg 1.417 r_angle_other_deg 0.947 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 6151 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing