3QPF

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 apo-structure


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
2.4750.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.04α = 90
b = 101.61β = 90
c = 158.89γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray117CCDMARMOSAIC 325 mm CCDRh coated flat mirror, toroidal focusing mirror2010-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97915SSRLBL9-2

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
12.1585.699509725097222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2799

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1548.3925097250972272999.980.160.159290.156230.21743RANDOM12.724
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]
-0.20.89-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.965
r_dihedral_angle_4_deg19.858
r_dihedral_angle_3_deg13.594
r_dihedral_angle_1_deg5.929
r_scangle_it3.913
r_scbond_it2.449
r_angle_refined_deg1.396
r_mcangle_it1.392
r_mcbond_it0.747
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.965
r_dihedral_angle_4_deg19.858
r_dihedral_angle_3_deg13.594
r_dihedral_angle_1_deg5.929
r_scangle_it3.913
r_scbond_it2.449
r_angle_refined_deg1.396
r_mcangle_it1.392
r_mcbond_it0.747
r_chiral_restr0.095
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 Atoms925
Heterogen Atoms68

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement