☰ Navigation Tabs
Bacteroides salyersiae GH164 beta-mannosidase 2-deoxy-2-fluoro-beta-D-mannosyl enzyme intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Ammonium tartrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.59 52.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.155 α = 91.977 b = 104.873 β = 97.733 c = 171.627 γ = 107.161
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 EIGER2 X 16M 2019-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.55 99.9 98.7 0.994 6.1 3.6 148606
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 0.458 1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6T50 2.55 89.337 148575 7529 98.643 0.215 0.2138 0.2139 0.2452 0.2454 49.969
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] 2.778 -0.942 -0.34 -0.228 0.413 -1.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 19.419 r_dihedral_angle_3_deg 17.894 r_dihedral_angle_1_deg 7.575 r_lrange_it 5.741 r_lrange_other 5.741 r_scangle_it 4.045 r_scangle_other 4.045 r_mcangle_it 3.862 r_mcangle_other 3.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 19.419 r_dihedral_angle_3_deg 17.894 r_dihedral_angle_1_deg 7.575 r_lrange_it 5.741 r_lrange_other 5.741 r_scangle_it 4.045 r_scangle_other 4.045 r_mcangle_it 3.862 r_mcangle_other 3.861 r_scbond_it 2.468 r_scbond_other 2.467 r_mcbond_it 2.437 r_mcbond_other 2.436 r_angle_refined_deg 1.548 r_angle_other_deg 1.255 r_symmetry_xyhbond_nbd_refined 0.253 r_nbd_other 0.241 r_nbd_refined 0.195 r_symmetry_nbd_other 0.177 r_symmetry_nbd_refined 0.171 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_14 0.074 r_ncsr_local_group_1 0.073 r_ncsr_local_group_11 0.072 r_ncsr_local_group_12 0.072 r_ncsr_local_group_13 0.072 r_ncsr_local_group_2 0.071 r_ncsr_local_group_5 0.071 r_ncsr_local_group_6 0.071 r_ncsr_local_group_7 0.071 r_ncsr_local_group_8 0.071 r_ncsr_local_group_10 0.071 r_ncsr_local_group_15 0.071 r_ncsr_local_group_3 0.07 r_ncsr_local_group_9 0.07 r_chiral_restr 0.068 r_ncsr_local_group_4 0.068 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31388 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing