4KY5

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23D at pH 7 and 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 DROP727728% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2244.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.132α = 90
b = 60.342β = 94.7
c = 38.333γ = 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 vertically-focusing at 6.6:1 demagnification2013-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X250.979NSLSX25

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
11.450990.04846.56.6278382783823
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)
11.41.4296.90.218.55.41362

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 3BDC1.432.282760827608139099.030.16370.16370.16240.1871RANDOM21.4628
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]
-0.04-0.050.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.541
r_sphericity_free15.718
r_dihedral_angle_3_deg15.01
r_sphericity_bonded13.011
r_rigid_bond_restr8.785
r_dihedral_angle_4_deg8.412
r_dihedral_angle_1_deg6.027
r_angle_refined_deg1.911
r_chiral_restr0.153
r_bond_refined_d0.019
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.541
r_sphericity_free15.718
r_dihedral_angle_3_deg15.01
r_sphericity_bonded13.011
r_rigid_bond_restr8.785
r_dihedral_angle_4_deg8.412
r_dihedral_angle_1_deg6.027
r_angle_refined_deg1.911
r_chiral_restr0.153
r_bond_refined_d0.019
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1034
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms26

Software

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