1NXC

Structure of mouse Golgi alpha-1,2-mannosidase IA reveals the molecular basis for substrate specificity among Class I enzymes (family 47 glycosidases)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298PEG4000, pH 4.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2544.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.288α = 90
b = 72.164β = 90
c = 129.571γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMSC Blue Confocal Optics2002-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.5162.50.0610.28197173142-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.511.630.1473

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.5162.58210869386368989.180.171740.170790.1897RANDOM8.55
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]
0.41-0.39-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.837
r_sphericity_free5.32
r_sphericity_bonded3.069
r_scangle_it2.587
r_scbond_it1.664
r_angle_refined_deg1.382
r_rigid_bond_restr1.334
r_mcangle_it1.104
r_angle_other_deg0.903
r_mcbond_it0.613
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.837
r_sphericity_free5.32
r_sphericity_bonded3.069
r_scangle_it2.587
r_scbond_it1.664
r_angle_refined_deg1.382
r_rigid_bond_restr1.334
r_mcangle_it1.104
r_angle_other_deg0.903
r_mcbond_it0.613
r_nbd_other0.234
r_symmetry_vdw_other0.226
r_nbd_refined0.22
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.124
r_symmetry_hbond_refined0.121
r_nbtor_other0.112
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3693
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms95

Software

Software
Software NamePurpose
EPMRphasing
REFMACrefinement
PROTEUM PLUSdata reduction