2BRP

Crystal structure of S. pneumoniae hyaluronate lyase in complex with W249b


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W3YPDB ENTRY 1W3Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.6954.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.195α = 90
b = 103.265β = 90
c = 103.261γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

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
124443.90.1212.95.32703523.3
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)
122.0710.70.921.12.9

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 1W3Y244.0227035132343.90.1780.1780.202RANDOM28.2
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]
-10.985.075.91
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.3
c_scangle_it3.15
c_scbond_it2.13
c_mcangle_it2.03
c_angle_deg1.3
c_mcbond_it1.28
c_improper_angle_d0.82
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.3
c_scangle_it3.15
c_scbond_it2.13
c_mcangle_it2.03
c_angle_deg1.3
c_mcbond_it1.28
c_improper_angle_d0.82
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5790
Nucleic Acid Atoms
Solvent Atoms560
Heterogen Atoms90

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing