3DDG

GOLGI MANNOSIDASE II complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)-2-hydroxy-1 phenylethyl]amino}methyl) methylpyrrolidin-2-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F18 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298PEG 8000, Tris, pH 7, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.189α = 90
b = 110.083β = 90
c = 138.96γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM2006-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.746098.70.040526.321109465108067
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.79810.4012.742.927137

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2F181.7420.02109293107873161998.720.1730.1660.1660.195RANDOM14.07
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.16
r_dihedral_angle_4_deg20.271
r_dihedral_angle_3_deg14.489
r_dihedral_angle_1_deg6.308
r_scangle_it4.104
r_scbond_it2.609
r_angle_refined_deg1.628
r_mcangle_it1.61
r_mcbond_it0.933
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.16
r_dihedral_angle_4_deg20.271
r_dihedral_angle_3_deg14.489
r_dihedral_angle_1_deg6.308
r_scangle_it4.104
r_scbond_it2.609
r_angle_refined_deg1.628
r_mcangle_it1.61
r_mcbond_it0.933
r_nbtor_refined0.312
r_symmetry_vdw_refined0.211
r_nbd_refined0.202
r_symmetry_hbond_refined0.192
r_chiral_restr0.182
r_xyhbond_nbd_refined0.145
r_bond_refined_d0.017
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8188
Nucleic Acid Atoms
Solvent Atoms1078
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
SAINTdata scaling
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
CNSphasing