3BUP

Golgi alpha-mannosidase II D341N acid-base catalyst mutant with bound mannose


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. Crystal soaked in PNP-mannose at 4C, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.67α = 90
b = 109.486β = 90
c = 138.584γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirrors2002-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.0320960.06811.67.86904466283
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)
12.032.0879.80.3444.133614

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 1HTY2.0319.796841666227234796.810.1540.1520.195RANDOM19.27
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]
-0.04-0.010.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.474
r_dihedral_angle_4_deg17.174
r_dihedral_angle_3_deg13.116
r_dihedral_angle_1_deg6.233
r_scangle_it2.844
r_scbond_it1.893
r_angle_refined_deg1.344
r_mcangle_it1.134
r_mcbond_it0.745
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.474
r_dihedral_angle_4_deg17.174
r_dihedral_angle_3_deg13.116
r_dihedral_angle_1_deg6.233
r_scangle_it2.844
r_scbond_it1.893
r_angle_refined_deg1.344
r_mcangle_it1.134
r_mcbond_it0.745
r_nbtor_refined0.306
r_symmetry_vdw_refined0.241
r_nbd_refined0.203
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.144
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8187
Nucleic Acid Atoms
Solvent Atoms1105
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
MAR345dtbdata collection
CNSphasing