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GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymethyl)-1,2,3,6-tetrahydro-3-pyridinol
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 293 0.1 M sodium succinate, pH 7.4
10 % PEG 3350 with microseeding
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.473 α = 90 b = 90.366 β = 90 c = 132.772 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 EIGER X 16M 2019-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.950 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 1.86 90.37 100 0.996 12.4 8.1 91011
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 1.86 1.89 100 0.705 1.3
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 1.86 74.31 86399 4527 99.95 0.1881 0.1859 0.1949 0.2328 0.2368 RANDOM 34.862
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] -2.47 2.32 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.554 r_dihedral_angle_4_deg 17.635 r_dihedral_angle_3_deg 13.98 r_dihedral_angle_1_deg 7.413 r_mcangle_it 3.85 r_mcbond_it 2.814 r_mcbond_other 2.812 r_angle_other_deg 2.347 r_angle_refined_deg 1.543 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.554 r_dihedral_angle_4_deg 17.635 r_dihedral_angle_3_deg 13.98 r_dihedral_angle_1_deg 7.413 r_mcangle_it 3.85 r_mcbond_it 2.814 r_mcbond_other 2.812 r_angle_other_deg 2.347 r_angle_refined_deg 1.543 r_chiral_restr 0.076 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 8065 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling PHASER phasing REFMAC refinement