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Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.2 M ammonium sulfate, 24% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.37 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.815 α = 90 b = 102.23 β = 90 c = 50.68 γ = 90
Symmetry Space Group P 21 21 2
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 XE 16M 2021-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97629 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.3 68.403 98.8 0.116 0.121 0.035 0.999 21.3 21.5 116329
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 84.9 0.8 0.998 0.586 0.631 4.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1UUQ 1.3 68.403 116260 5818 98.636 0.126 0.1246 0.1577 0.1569 15.895
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] -1.399 0.962 0.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.852 r_dihedral_angle_4_deg 15.457 r_dihedral_angle_3_deg 11.442 r_dihedral_angle_1_deg 6.245 r_rigid_bond_restr 4.168 r_scangle_it 3.918 r_scangle_other 3.917 r_lrange_it 3.57 r_lrange_other 3.436 r_scbond_it 3.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.852 r_dihedral_angle_4_deg 15.457 r_dihedral_angle_3_deg 11.442 r_dihedral_angle_1_deg 6.245 r_rigid_bond_restr 4.168 r_scangle_it 3.918 r_scangle_other 3.917 r_lrange_it 3.57 r_lrange_other 3.436 r_scbond_it 3.427 r_scbond_other 3.426 r_mcangle_other 2.301 r_mcangle_it 2.293 r_mcbond_it 2.075 r_angle_refined_deg 1.917 r_mcbond_other 1.848 r_angle_other_deg 1.623 r_nbd_other 0.265 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.224 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.117 r_symmetry_xyhbond_nbd_refined 0.089 r_symmetry_nbtor_other 0.088 r_chiral_restr_other 0.075 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3292 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling MOLREP phasing Coot model building REFMAC refinement XDS data reduction