3DX0

Golgi alpha-Mannosidase II in complex with Mannostatin A at pH 5.75


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HTYPDB entry 1HTY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298PEG8000, Tris, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7
Crystal Properties
Matthews coefficientSolvent content
2.244.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.853α = 90
b = 109.86β = 90
c = 139.136γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 60002006-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54182

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
11.74099.60.054417.34.9116271
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)
11.71.7394.80.332.12.34090

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 1HTY1.719.57116441116104172499.710.160.160.186RANDOM13.239
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_1_deg6.128
r_scangle_it4.105
r_scbond_it2.537
r_mcangle_it1.58
r_angle_refined_deg1.56
r_mcbond_it0.893
r_symmetry_vdw_refined0.232
r_nbd_refined0.2
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.128
r_scangle_it4.105
r_scbond_it2.537
r_mcangle_it1.58
r_angle_refined_deg1.56
r_mcbond_it0.893
r_symmetry_vdw_refined0.232
r_nbd_refined0.2
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.129
r_chiral_restr0.118
r_bond_refined_d0.017
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8188
Nucleic Acid Atoms
Solvent Atoms1163
Heterogen Atoms39

Software

Software
Software NamePurpose
SAINTdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SADABSdata scaling
CNSphasing