3BVT

GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl (alpha-D-mannopyranosyl)-(1->3)-S-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 for 24 hrs, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.04α = 90
b = 109.847β = 90
c = 138.627γ = 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 A10.977CHESSA1

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
11.32099.80.06812.96.7256778256264
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)
11.31.3399.60.8872.65.516843

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 1HTY1.319.84257039256139380199.650.1740.1740.192RANDOM16.953
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_deg37.004
r_dihedral_angle_4_deg18.705
r_dihedral_angle_3_deg12.16
r_dihedral_angle_1_deg6.087
r_scangle_it3.539
r_scbond_it2.32
r_mcangle_it1.636
r_angle_refined_deg1.52
r_mcbond_it1.031
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.004
r_dihedral_angle_4_deg18.705
r_dihedral_angle_3_deg12.16
r_dihedral_angle_1_deg6.087
r_scangle_it3.539
r_scbond_it2.32
r_mcangle_it1.636
r_angle_refined_deg1.52
r_mcbond_it1.031
r_nbtor_refined0.311
r_symmetry_vdw_refined0.212
r_nbd_refined0.203
r_xyhbond_nbd_refined0.142
r_symmetry_hbond_refined0.116
r_chiral_restr0.101
r_metal_ion_refined0.019
r_bond_refined_d0.014
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8194
Nucleic Acid Atoms
Solvent Atoms1453
Heterogen Atoms68

Software

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