2QGR

Structure of the R178A mutant of delta PDZ DegS protease


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529350 mM NaCacodylate pH 6.5, 100 mM NaCitrate, 20% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.216α = 90
b = 70.216β = 90
c = 119.228γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123IMAGE PLATERIGAKU RAXIS IVVarimax-HR2007-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.75098.25938
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)
12.72.887.50.201

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2QF02.729.46539431389.30.2490.26292.57
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]
-30.396-30.39660.792
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.01
f_bond_d0.002
f_bond_d_na
f_bond_d_prot
f_angle_d
f_angle_d_na
f_angle_d_prot
f_angle_deg
f_angle_deg_na
f_angle_deg_prot
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.01
f_bond_d0.002
f_bond_d_na
f_bond_d_prot
f_angle_d
f_angle_d_na
f_angle_d_prot
f_angle_deg
f_angle_deg_na
f_angle_deg_prot
f_dihedral_angle_d_na
f_dihedral_angle_d_prot
f_improper_angle_d
f_improper_angle_d_na
f_improper_angle_d_prot
f_mcbond_it
f_mcangle_it
f_scbond_it
f_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1238
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
DENZOdata reduction