5A6J

GH20C, Beta-hexosaminidase from Streptococcus pneumoniae


X-RAY DIFFRACTION

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
2.2244.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.84α = 90
b = 136.94β = 90
c = 202.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291CCDRIGAKU R-AXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-002

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
11.9450.797.40.119.23.81842852
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)
11.942.0596.90.343.93.7

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 2EPN1.94113.41174931926997.220.208530.205910.2579RANDOM19.831
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]
0.82-1.320.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.947
r_dihedral_angle_4_deg16.946
r_dihedral_angle_3_deg12.988
r_dihedral_angle_1_deg6.228
r_mcangle_it1.594
r_angle_refined_deg1.283
r_scbond_it1.022
r_mcbond_it0.977
r_mcbond_other0.977
r_angle_other_deg0.792
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.947
r_dihedral_angle_4_deg16.946
r_dihedral_angle_3_deg12.988
r_dihedral_angle_1_deg6.228
r_mcangle_it1.594
r_angle_refined_deg1.283
r_scbond_it1.022
r_mcbond_it0.977
r_mcbond_other0.977
r_angle_other_deg0.792
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms19496
Nucleic Acid Atoms
Solvent Atoms1619
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing