1ODU

CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA-FUCOSIDASE IN COMPLEX WITH FUCOSE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HL8NATIVE ALPHA-L-FUCOSIDASE, PDB ENTRY 1HL8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1818% PEG600, 5% JEFFAMINE M-600, 100 MM TRIS-HCL PH 8.0, PROTEIN CONCENTRATION 5 MG/ML FUCOSE WAS INTRODUCED BY SHORT SOAKING OF A NATIVE
Crystal Properties
Matthews coefficientSolvent content
2.7454.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 179.08α = 90
b = 179.08β = 90
c = 174.692γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2001-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.857.798.10.0566.83.924598100.81
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)
12.82.8798.10.4421.63.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNATIVE ALPHA-L-FUCOSIDASE, PDB ENTRY 1HL82.819.7624054184897.50.2030.2010.23RANDOM
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]
-2.32-1.16-2.333.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.968
r_scangle_it0.989
r_angle_refined_deg0.987
r_angle_other_deg0.757
r_mcangle_it0.573
r_scbond_it0.567
r_mcbond_it0.304
r_nbd_other0.212
r_symmetry_vdw_other0.2
r_symmetry_hbond_refined0.193
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.968
r_scangle_it0.989
r_angle_refined_deg0.987
r_angle_other_deg0.757
r_mcangle_it0.573
r_scbond_it0.567
r_mcbond_it0.304
r_nbd_other0.212
r_symmetry_vdw_other0.2
r_symmetry_hbond_refined0.193
r_nbd_refined0.17
r_xyhbond_nbd_refined0.136
r_symmetry_vdw_refined0.091
r_nbtor_other0.082
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_other0.007
r_bond_other_d0.005
r_gen_planes_refined0.005
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7004
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing