3N04

THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (FAMILY 31) FROM RUMINOCOCCUS OBEUM ATCC 29174


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52890.1M BIS-TRIS 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3146.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.861α = 90
b = 124.97β = 107.74
c = 88.601γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirror2008-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929APS19-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
12.024499.90.14914.84.69320093200
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)
2.022.0799.60.6442.284.4

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 DIFFRACTIONSADTHROUGHOUT2.0243.98842788427465599.130.170320.168390.20675RANDOM23.886
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]
-0.290.03-0.050.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.73
r_dihedral_angle_4_deg17.37
r_dihedral_angle_3_deg14.873
r_dihedral_angle_1_deg6.084
r_scangle_it3.247
r_scbond_it2.015
r_angle_refined_deg1.275
r_mcangle_it1.172
r_mcbond_it0.608
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.73
r_dihedral_angle_4_deg17.37
r_dihedral_angle_3_deg14.873
r_dihedral_angle_1_deg6.084
r_scangle_it3.247
r_scbond_it2.015
r_angle_refined_deg1.275
r_mcangle_it1.172
r_mcbond_it0.608
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10872
Nucleic Acid Atoms
Solvent Atoms824
Heterogen Atoms18

Software

Software
Software NamePurpose
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing