6RRN

GOLGI ALPHA-MANNOSIDASE II in complex with pentyl 2,5-dideoxy-2,5-imino-D-talo-hexonamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BUB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M sodium succinate, pH 7.4 10 % PEG 3350 with microseeding
Crystal Properties
Matthews coefficientSolvent content
2.346.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.71α = 90
b = 90.386β = 90
c = 130.274γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5990.391000.99710.37.9140967
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.621000.7171.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3bub1.5974.37133775708899.950.18140.17990.2096RANDOM22.518
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]
-1.261.080.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.982
r_dihedral_angle_4_deg17.315
r_dihedral_angle_3_deg12.554
r_dihedral_angle_1_deg6.976
r_mcangle_it2.624
r_angle_other_deg2.348
r_mcbond_it1.935
r_mcbond_other1.933
r_angle_refined_deg1.688
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.982
r_dihedral_angle_4_deg17.315
r_dihedral_angle_3_deg12.554
r_dihedral_angle_1_deg6.976
r_mcangle_it2.624
r_angle_other_deg2.348
r_mcbond_it1.935
r_mcbond_other1.933
r_angle_refined_deg1.688
r_chiral_restr0.09
r_bond_other_d0.035
r_gen_planes_other0.019
r_bond_refined_d0.012
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7983
Nucleic Acid Atoms
Solvent Atoms649
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling
REFMACrefinement
PHASERphasing