3BVV

Golgi mannosidase II D204A catalytic nucleophile mutant complex with METHYL ALPHA-D-MANNOPYRANOSYL-(1->3)-[6-THIO-ALPHA-D-MANNOPYRANOSYL-(1->6)]-BETA-D-MANNOPYRANOSIDE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HTYPDB entry 1HTY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293TRIS, NACL, PEG6000, MPD. Crystals washed in phosphate buffered reservoir solution before soaking with substrate for 24 hrs, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.104α = 90
b = 109.815β = 90
c = 139.303γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.972CHESSA1

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
11.32097.80.0817.27.6260486254755
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)
1.31.3278.40.264.83.6

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1HTY1.319.61260346254592379697.790.1530.1520.173RANDOM16.368
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.988
r_dihedral_angle_4_deg17.691
r_dihedral_angle_3_deg12.439
r_dihedral_angle_1_deg6.201
r_sphericity_free4.005
r_scangle_it3.45
r_sphericity_bonded3.401
r_scbond_it2.43
r_mcangle_it1.799
r_angle_refined_deg1.461
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.988
r_dihedral_angle_4_deg17.691
r_dihedral_angle_3_deg12.439
r_dihedral_angle_1_deg6.201
r_sphericity_free4.005
r_scangle_it3.45
r_sphericity_bonded3.401
r_scbond_it2.43
r_mcangle_it1.799
r_angle_refined_deg1.461
r_rigid_bond_restr1.447
r_mcbond_it1.257
r_nbtor_refined0.309
r_nbd_refined0.204
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_refined0.142
r_symmetry_hbond_refined0.136
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_metal_ion_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8581
Nucleic Acid Atoms
Solvent Atoms1706
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing