5AC4

GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with GalNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EPNPDB ENTRY 2EPN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110.212% (W/V) PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.05 M CAPS, PH 10.2, 1% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.1943.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.55α = 90
b = 99.05β = 90
c = 133.45γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291CCDMARMOSAIC 325 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
12.0879.5498.20.120.111.1749992
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)
12.082.19960.396.29.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2EPN2.08133.4571296366197.790.163250.161470.1984RANDOM17.666
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]
-0.140.41-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.343
r_dihedral_angle_4_deg17.546
r_dihedral_angle_3_deg12.429
r_dihedral_angle_1_deg6.195
r_mcangle_it1.407
r_scbond_it1.365
r_angle_refined_deg1.334
r_mcbond_it0.881
r_mcbond_other0.881
r_angle_other_deg0.855
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.343
r_dihedral_angle_4_deg17.546
r_dihedral_angle_3_deg12.429
r_dihedral_angle_1_deg6.195
r_mcangle_it1.407
r_scbond_it1.365
r_angle_refined_deg1.334
r_mcbond_it0.881
r_mcbond_other0.881
r_angle_other_deg0.855
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms10029
Nucleic Acid Atoms
Solvent Atoms622
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing