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Structure of GH1 Br2 beta-glucosidase E163Q mutant from bovine rumen metagenome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other E350G mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277 0.1M sodium acetate trihydrate pH 7.4, 1.6M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.58 51.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.489 α = 90 b = 113.416 β = 90 c = 180.493 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 CCD ADSC QUANTUM 315r 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.9762 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 2.095 50 90.3 0.097 0.109 0.997 10.25 4.9 115105 46.445
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.095 2.22 96.4 0.898 1.008 0.625 1.55 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.095 48.139 115104 1990 90.313 0.227 0.2267 0.2314 0.2613 0.2655 48
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] -0.681 0.454 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.016 r_dihedral_angle_3_deg 13.9 r_dihedral_angle_4_deg 13.754 r_dihedral_angle_1_deg 6.913 r_lrange_it 5.94 r_lrange_other 5.929 r_scangle_it 4.217 r_scangle_other 4.18 r_mcangle_it 4.02 r_mcangle_other 4.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.016 r_dihedral_angle_3_deg 13.9 r_dihedral_angle_4_deg 13.754 r_dihedral_angle_1_deg 6.913 r_lrange_it 5.94 r_lrange_other 5.929 r_scangle_it 4.217 r_scangle_other 4.18 r_mcangle_it 4.02 r_mcangle_other 4.02 r_mcbond_it 2.732 r_mcbond_other 2.73 r_scbond_it 2.721 r_scbond_other 2.697 r_angle_refined_deg 1.249 r_angle_other_deg 1.205 r_nbd_other 0.259 r_symmetry_nbd_refined 0.22 r_nbd_refined 0.198 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_other 0.166 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.054 r_ncsr_local_group_1 0.046 r_ncsr_local_group_4 0.044 r_ncsr_local_group_6 0.044 r_ncsr_local_group_2 0.041 r_ncsr_local_group_3 0.041 r_ncsr_local_group_5 0.04 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14439 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing