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GOLGI ALPHA-MANNOSIDASE II in complex with (5R,6R,7S,8S)-5,6,7,8-tetrahydro-5-(hydroxymethyl)-3-(3-phenylpropyl)imidazo[1,2-a]pyridine-6,7,8-triol
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 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.959 α = 90 b = 91.908 β = 90 c = 131.835 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 1.9 91.91 100 0.998 10.2 6.9 85812
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 1.9 1.93 0.87 1.9
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 1.9 75.51 81411 4306 99.93 0.1946 0.1922 0.1995 0.2419 0.2459 RANDOM 31.282
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] -2.68 2 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.995 r_dihedral_angle_4_deg 17.572 r_dihedral_angle_3_deg 14.842 r_dihedral_angle_1_deg 7.497 r_mcangle_it 3.667 r_mcbond_it 2.611 r_mcbond_other 2.611 r_angle_other_deg 2.324 r_angle_refined_deg 1.54 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.995 r_dihedral_angle_4_deg 17.572 r_dihedral_angle_3_deg 14.842 r_dihedral_angle_1_deg 7.497 r_mcangle_it 3.667 r_mcbond_it 2.611 r_mcbond_other 2.611 r_angle_other_deg 2.324 r_angle_refined_deg 1.54 r_chiral_restr 0.074 r_bond_other_d 0.035 r_gen_planes_other 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8062 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling PHASER phasing