4N31

Structure and activity of Streptococcus pyogenes SipA: a signal peptidase homologue essential for pilus polymerisation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K8W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72911M NaKPO4 pH 7.0, 8% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.6666.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.811α = 90
b = 132.811β = 90
c = 107.156γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315Adaptive and mechanically bent Si mirrors2011-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95468Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.228.7599.540.1270.12728.342.7288602886050.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3197.53.6553.71.341.44006

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4K8W2.228.752747027299148799.380.202310.200890.22933RANDOM46.584
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]
-0.03-0.01-0.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.359
r_dihedral_angle_3_deg16.053
r_dihedral_angle_4_deg15.053
r_dihedral_angle_1_deg8.08
r_angle_refined_deg1.559
r_angle_other_deg0.782
r_chiral_restr0.096
r_gen_planes_refined0.016
r_bond_refined_d0.011
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.359
r_dihedral_angle_3_deg16.053
r_dihedral_angle_4_deg15.053
r_dihedral_angle_1_deg8.08
r_angle_refined_deg1.559
r_angle_other_deg0.782
r_chiral_restr0.096
r_gen_planes_refined0.016
r_bond_refined_d0.011
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2158
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms49

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling