3BUD

Golgi mannosidase II D204A catalytic nucleophile mutant with an empty active site


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; Tris found in the active site under normal crystallization conditions was removed by soaking crystals in phosphate buffered resevoir solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.903α = 90
b = 109.478β = 90
c = 138.501γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2003-11-12MSINGLE 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
11.853099.80.05418.87.3900968937228.1
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)
11.851.8998.60.314.34.35801

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 1HTY1.8519.989009689235360799.040.1580.1570.192RANDOM18.932
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]
0.02-0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.859
r_dihedral_angle_4_deg18.458
r_dihedral_angle_3_deg12.722
r_dihedral_angle_1_deg6.18
r_scangle_it2.95
r_scbond_it1.905
r_angle_refined_deg1.32
r_mcangle_it1.224
r_mcbond_it0.809
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.859
r_dihedral_angle_4_deg18.458
r_dihedral_angle_3_deg12.722
r_dihedral_angle_1_deg6.18
r_scangle_it2.95
r_scbond_it1.905
r_angle_refined_deg1.32
r_mcangle_it1.224
r_mcbond_it0.809
r_nbtor_refined0.305
r_symmetry_vdw_refined0.247
r_nbd_refined0.201
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.154
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8194
Nucleic Acid Atoms
Solvent Atoms1498
Heterogen Atoms44

Software

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