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GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benzodioxepin-7-yl)benzyl]oxy}pentyl)-2-(hydroxymethyl)-3,4,5-piperidinetriol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M sodium succinate, pH 7.4
10 % PEG 3350 with microseeding
Crystal Properties Matthews coefficient Solvent content 2.35 47.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.171 α = 90 b = 91.671 β = 90 c = 132.316 γ = 90
Symmetry Space Group P 21 21 21
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 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.915 Diamond I04
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 2.15 75.47 97.6 0.998 9.2 7 57896
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 2.15 2.21 98.8 0.787 1.6 6.8
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 (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 3bub 2.15 75.47 54910 2823 96.71 0.2026 0.1995 0.2069 0.265 0.2697 RANDOM 41.175
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] -4.24 2.58 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.507 r_dihedral_angle_4_deg 21.489 r_dihedral_angle_3_deg 16.361 r_dihedral_angle_1_deg 8.061 r_mcangle_it 5.065 r_mcbond_it 3.611 r_mcbond_other 3.607 r_angle_other_deg 2.342 r_angle_refined_deg 1.616 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.507 r_dihedral_angle_4_deg 21.489 r_dihedral_angle_3_deg 16.361 r_dihedral_angle_1_deg 8.061 r_mcangle_it 5.065 r_mcbond_it 3.611 r_mcbond_other 3.607 r_angle_other_deg 2.342 r_angle_refined_deg 1.616 r_chiral_restr 0.073 r_bond_other_d 0.035 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8113 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling PHASER phasing