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Crystal structure of alpha-1,2-mannosidase from Caulobacter K31 strain in complex with 1-deoxymannojirimycin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium acetate, 22% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.05 39.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.371 α = 90 b = 145.371 β = 90 c = 50.838 γ = 120
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 2015-11-28 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) 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 0.95 47.14 98.9 1 17.2 4.3 249654
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.97 91 0.49 0.63 1.7 2.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 0.95 47.14 237036 12618 98.83 0.0917 0.09109 0.0908 0.1032 0.1028 RANDOM 10.764
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] 0.17 0.08 0.17 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.337 r_sphericity_free 29.977 r_dihedral_angle_4_deg 17.623 r_dihedral_angle_3_deg 12.07 r_sphericity_bonded 10.146 r_dihedral_angle_1_deg 6.417 r_rigid_bond_restr 5.413 r_scangle_other 4.633 r_scbond_it 4.498 r_scbond_other 4.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.337 r_sphericity_free 29.977 r_dihedral_angle_4_deg 17.623 r_dihedral_angle_3_deg 12.07 r_sphericity_bonded 10.146 r_dihedral_angle_1_deg 6.417 r_rigid_bond_restr 5.413 r_scangle_other 4.633 r_scbond_it 4.498 r_scbond_other 4.497 r_long_range_B_other 3.948 r_long_range_B_refined 3.946 r_angle_refined_deg 2.038 r_mcangle_other 1.938 r_mcangle_it 1.937 r_mcbond_it 1.341 r_mcbond_other 1.317 r_angle_other_deg 1.086 r_chiral_restr 0.119 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3472 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling