6VJB

Crystal structure of a catalytically inactive CXC Chemokine-degrading protease SpyCEP from Streptococcus pyogenes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5XYR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M ammonium formate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3847.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.5α = 90
b = 121.75β = 111.78
c = 106.64γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.93940ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.28996.60.080.110.080.996.22.27694835.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.242.2978.60.560.790.560.561.62

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 REPLACEMENTTHROUGHOUT5xyr2.2444.5176942391196.50.1930.190.244RANDOM52.34
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]
3.52673.7747-3.3406-0.1862
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.27
t_omega_torsion2.99
t_angle_deg1.15
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.27
t_omega_torsion2.99
t_angle_deg1.15
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10461
Nucleic Acid Atoms
Solvent Atoms691
Heterogen Atoms43

Software

Software
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing