1X9D

Crystal Structure Of Human Class I alpha-1,2-Mannosidase In Complex With Thio-Disaccharide Substrate Analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FMIPDB ENTRY 1FMI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529824% PEG 4000, 50mM ammonium sulfate, 0.1M MES, 10% 1,4-butanediol, pH 6.5, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9336.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.687α = 89.49
b = 53.878β = 63.6
c = 56.234γ = 62.61
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.99985APS22-ID

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
11.415095.50.10284600
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)
1.411.4693.20.129

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FMI1.4148.876092850795.450.1460.145980.1440.162RANDOM8.368
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]
0.26-0.25-0.02-0.070.020.05
RMS Deviations
KeyRefinement Restraint Deviation
TORSION ANGLES, PERIOD 2 (DEGREES)32.283
TORSION ANGLES, PERIOD 4 (DEGREES)13.33
r_dihedral_angle_2_deg11.599
r_dihedral_angle_1_deg5.907
r_scangle_it3.505
r_scbond_it2.439
r_mcangle_it2.257
r_mcbond_it1.717
r_angle_refined_deg1.337
r_angle_other_deg0.826
RMS Deviations
KeyRefinement Restraint Deviation
TORSION ANGLES, PERIOD 2 (DEGREES)32.283
TORSION ANGLES, PERIOD 4 (DEGREES)13.33
r_dihedral_angle_2_deg11.599
r_dihedral_angle_1_deg5.907
r_scangle_it3.505
r_scbond_it2.439
r_mcangle_it2.257
r_mcbond_it1.717
r_angle_refined_deg1.337
r_angle_other_deg0.826
MAIN-CHAIN BOND OTHER ATOMS (A**2)0.499
r_symmetry_vdw_other0.24
r_nbd_refined0.22
NON-BONDED TORSION REFINED ATOMS (A)0.184
r_nbd_other0.167
r_symmetry_vdw_refined0.155
r_xyhbond_nbd_refined0.095
r_chiral_restr0.087
r_nbtor_other0.082
r_symmetry_hbond_refined0.069
POTENTIAL METAL-ION REFINED ATOMS (A)0.045
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3668
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms35

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
EPMRphasing