2WWD

3D-structure of the modular autolysin LytC from Streptococcus pneumoniae in complex with pneummococcal peptidoglycan fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WW5PDB ENTRY 2WW5

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.7455.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.4α = 90
b = 66.87β = 105.77
c = 77.92γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.257599.40.0812.73.527909
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)
12.252.3799.80.52.63.6

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 2WW52.2557.1725982192599.30.2060.2040.232RANDOM38.15
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]
0.580.73-0.420.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.205
r_dihedral_angle_4_deg23.612
r_dihedral_angle_3_deg14.444
r_dihedral_angle_1_deg5.465
r_scangle_it1.802
r_scbond_it1.158
r_angle_refined_deg1.097
r_mcangle_it0.981
r_mcbond_it0.542
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.205
r_dihedral_angle_4_deg23.612
r_dihedral_angle_3_deg14.444
r_dihedral_angle_1_deg5.465
r_scangle_it1.802
r_scbond_it1.158
r_angle_refined_deg1.097
r_mcangle_it0.981
r_mcbond_it0.542
r_nbtor_refined0.308
r_symmetry_vdw_refined0.211
r_nbd_refined0.196
r_symmetry_hbond_refined0.148
r_xyhbond_nbd_refined0.133
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms3653
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing