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Bacteroides salyersiae GH164 beta-mannosidase in complex with noeuromycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T5O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M ammonium tartrate pH 7.0, 13 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.59 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.754 α = 92.602 b = 105.096 β = 97.209 c = 170.544 γ = 105.096
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-F 2019-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.916 Diamond I04-1
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 2.06 101.13 98.3 0.986 5.2 3.5 280992
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 2.06 2.1 0.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6T5O 2.06 90.191 280985 13971 98.228 0.214 0.2122 0.2122 0.2399 0.2399 44.862
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] 1.755 0.496 -0.979 -0.093 0.21 -1.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.764 r_dihedral_angle_4_deg 24.434 r_dihedral_angle_3_deg 16.356 r_dihedral_angle_1_deg 7.739 r_lrange_it 5.166 r_lrange_other 5.158 r_scangle_it 3.123 r_scangle_other 3.123 r_mcangle_it 2.875 r_mcangle_other 2.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.764 r_dihedral_angle_4_deg 24.434 r_dihedral_angle_3_deg 16.356 r_dihedral_angle_1_deg 7.739 r_lrange_it 5.166 r_lrange_other 5.158 r_scangle_it 3.123 r_scangle_other 3.123 r_mcangle_it 2.875 r_mcangle_other 2.875 r_scbond_it 1.879 r_scbond_other 1.879 r_mcbond_it 1.799 r_mcbond_other 1.799 r_angle_refined_deg 1.613 r_angle_other_deg 1.368 r_nbd_other 0.239 r_nbd_refined 0.204 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.148 r_symmetry_nbd_refined 0.125 r_chiral_restr_other 0.081 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.08 r_ncsr_local_group_10 0.079 r_ncsr_local_group_4 0.078 r_ncsr_local_group_13 0.075 r_ncsr_local_group_14 0.075 r_ncsr_local_group_2 0.074 r_ncsr_local_group_8 0.074 r_ncsr_local_group_1 0.073 r_ncsr_local_group_3 0.073 r_ncsr_local_group_5 0.073 r_ncsr_local_group_9 0.073 r_ncsr_local_group_12 0.073 r_ncsr_local_group_15 0.073 r_ncsr_local_group_7 0.072 r_ncsr_local_group_6 0.071 r_ncsr_local_group_11 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31476 Nucleic Acid Atoms Solvent Atoms 1029 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling PHASER phasing