3QRY

Analysis of a new family of widely distributed metal-independent alpha mannosidases provides unique insight into the processing of N-linked glycans, Streptococcus pneumoniae SP_2144 1-deoxymannojirimycin complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP80.1 M Hepes, 1.2 M LiSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.4850.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.46α = 90
b = 158.8β = 107.19
c = 60.04γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray117CCDMARMOSAIC 325 mm CCD2010-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.75158.899888188881822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.842

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT1.752028881888818467997.40.172060.169590.21845RANDOM13.151
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]
1.740.63-0.99-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.382
r_dihedral_angle_4_deg16.816
r_dihedral_angle_3_deg12.927
r_dihedral_angle_1_deg5.868
r_scangle_it3.571
r_scbond_it2.232
r_angle_refined_deg1.401
r_mcangle_it1.28
r_mcbond_it0.748
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.382
r_dihedral_angle_4_deg16.816
r_dihedral_angle_3_deg12.927
r_dihedral_angle_1_deg5.868
r_scangle_it3.571
r_scbond_it2.232
r_angle_refined_deg1.401
r_mcangle_it1.28
r_mcbond_it0.748
r_chiral_restr0.099
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6922
Nucleic Acid Atoms
Solvent Atoms1388
Heterogen Atoms46

Software

Software
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement
SCALAdata scaling