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GOLGI ALPHA-MANNOSIDASE II in complex with pentyl 2,5-dideoxy-2,5-imino-D-talo-hexonamide
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 2.3 46.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.71 α = 90 b = 90.386 β = 90 c = 130.274 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 2018-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.59 90.39 100 0.997 10.3 7.9 140967
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 1.59 1.62 100 0.717 1.7
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 1.59 74.37 133775 7088 99.95 0.1814 0.1799 0.1893 0.2096 0.2159 RANDOM 22.518
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] -1.26 1.08 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.982 r_dihedral_angle_4_deg 17.315 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 6.976 r_mcangle_it 2.624 r_angle_other_deg 2.348 r_mcbond_it 1.935 r_mcbond_other 1.933 r_angle_refined_deg 1.688 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.982 r_dihedral_angle_4_deg 17.315 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 6.976 r_mcangle_it 2.624 r_angle_other_deg 2.348 r_mcbond_it 1.935 r_mcbond_other 1.933 r_angle_refined_deg 1.688 r_chiral_restr 0.09 r_bond_other_d 0.035 r_gen_planes_other 0.019 r_bond_refined_d 0.012 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7983 Nucleic Acid Atoms Solvent Atoms 649 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling REFMAC refinement PHASER phasing