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Structure of a GH3 b-glIcosidase from cow rumen metagenome in complex with glucose
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 5.5 291 25% PEG 3350, 0.2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, then soaked in 20% glucose.
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.631 α = 90 b = 119.182 β = 90 c = 157.417 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 2014-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9786 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.17 95.02 99.7 0.127 0.995 11 6.6 51199
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 2.17 2.24 99.9 0.579 3.3 6.6
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 5K6L 2.17 95.02 48548 2584 99.56 0.17699 0.17484 0.1826 0.21824 0.2218 RANDOM 31.178
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] 5.29 -2.83 -2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.566 r_dihedral_angle_4_deg 13.552 r_dihedral_angle_3_deg 12.251 r_dihedral_angle_1_deg 6.148 r_long_range_B_refined 4.164 r_long_range_B_other 4.081 r_scangle_other 2.676 r_mcangle_it 2.156 r_mcangle_other 2.156 r_scbond_it 1.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.566 r_dihedral_angle_4_deg 13.552 r_dihedral_angle_3_deg 12.251 r_dihedral_angle_1_deg 6.148 r_long_range_B_refined 4.164 r_long_range_B_other 4.081 r_scangle_other 2.676 r_mcangle_it 2.156 r_mcangle_other 2.156 r_scbond_it 1.572 r_scbond_other 1.572 r_mcbond_it 1.27 r_mcbond_other 1.27 r_angle_refined_deg 1.218 r_angle_other_deg 0.878 r_chiral_restr 0.069 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 6121 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing