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Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured cyclophellitol aziridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.7 291 PEG 3350, sodium bromide, MES buffer
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.92 α = 90 b = 116.858 β = 114.15 c = 100.844 γ = 90
Symmetry Space Group P 1 21 1
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 2016-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 2.05 92.19 98.6 0.049 0.997 8.9 4.1 119933
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 97.9 0.522 0.535 4
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 2JE8 2.05 92.19 113966 5938 98.47 0.1877 0.1854 0.1934 0.2333 0.2391 RANDOM 33.93
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] -0.85 -0.1 -0.68 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.203 r_dihedral_angle_4_deg 17.925 r_dihedral_angle_3_deg 14.612 r_dihedral_angle_1_deg 7.482 r_angle_refined_deg 1.578 r_angle_other_deg 1.248 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.203 r_dihedral_angle_4_deg 17.925 r_dihedral_angle_3_deg 14.612 r_dihedral_angle_1_deg 7.482 r_angle_refined_deg 1.578 r_angle_other_deg 1.248 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13496 Nucleic Acid Atoms Solvent Atoms 902 Heterogen Atoms 199
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling REFMAC phasing