4KD3

Crystal structure of Staphylococcal nuclease variant Delta+PHS L25A/V66A/I92A at cryogenic temperature


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BDCPDB ENTRY 3BDC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627720% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2344.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.078α = 90
b = 60.042β = 94.88
c = 38.478γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMeridionally-bent fused silica mirror with palladium and uncoated stripes verti cally-focusing at 6.6:1 demagnification2011-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.9790NSLSX25

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
11.755099.60.043216.3142811428134.3
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)
11.751.781000.11417.76.5712

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3BDC1.7538.34142651426571799.330.18260.18260.18070.2191RANDOM28.9653
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]
-2.130.74-1.333.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.53
r_dihedral_angle_3_deg17.681
r_dihedral_angle_4_deg11.589
r_dihedral_angle_1_deg6.201
r_angle_refined_deg1.949
r_chiral_restr0.144
r_bond_refined_d0.019
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1025
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms26

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction