☰ Navigation Tabs
GOLGI ALPHA-MANNOSIDASE II in complex with 5-(Adamantan-1yl-methoxy)-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 7.0
10 % PEG 3350 with microseeding
Crystal Properties Matthews coefficient Solvent content 2.35 47.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.354 α = 90 b = 91.517 β = 90 c = 132.748 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 1.95 91.52 100 0.997 9.5 7.9 631798 80011
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 1.95 1.99 0.812 1.2
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 1.95 75.46 75956 3974 99.96 0.2027 0.2 0.2082 0.2535 0.2546 RANDOM 41.666
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] -4.49 5.51 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.915 r_dihedral_angle_4_deg 19.026 r_dihedral_angle_3_deg 15.17 r_dihedral_angle_1_deg 7.984 r_mcangle_it 4.847 r_mcbond_it 3.371 r_mcbond_other 3.37 r_angle_other_deg 2.338 r_angle_refined_deg 1.524 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.915 r_dihedral_angle_4_deg 19.026 r_dihedral_angle_3_deg 15.17 r_dihedral_angle_1_deg 7.984 r_mcangle_it 4.847 r_mcbond_it 3.371 r_mcbond_other 3.37 r_angle_other_deg 2.338 r_angle_refined_deg 1.524 r_chiral_restr 0.069 r_bond_other_d 0.035 r_gen_planes_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8106 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction Aimless data scaling PHASER phasing