3BVU

GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl(alpha-D-mannopyranosyl)-(1->3)-S-[(alpha-D-mannopyranosyl)-(1->6)]-alpha-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, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.992α = 90
b = 109.786β = 90
c = 139.049γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1

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
11.122099.50.0778.87.44019723999620.142
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)
11.121.1598.50.6282.5526166

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 REPLACEMENTFREE RPDB entry 1HTY1.1220401800394166606798.10.1140.1140.155RANDOM19.609
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
s_approx_iso_adps0.108
s_zero_chiral_vol0.087
s_non_zero_chiral_vol0.087
s_similar_adp_cmpnt0.054
s_angle_d0.031
s_from_restr_planes0.03
s_anti_bump_dis_restr0.026
s_bond_d0.015
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8185
Nucleic Acid Atoms
Solvent Atoms1499
Heterogen Atoms63

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CNSphasing
SHELXL-97refinement