3SK4

Crystal structure of Staphylococcal nuclease variant Delta+PHS D21N/V23E 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 DROP827725% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2545.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.213α = 90
b = 60.51β = 94.38
c = 38.626γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER APEX IImulti-layer optics2010-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER

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
11.8560.511000.03232912.5123091230928.1
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)
11.851.881000.33875.01

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 3BDC1.8531.12122931229358699.990.17660.17660.17420.2275RANDOM22.4439
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]
-0.080.05-0.080.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.318
r_dihedral_angle_3_deg15.88
r_dihedral_angle_1_deg6.597
r_dihedral_angle_4_deg5.097
r_scangle_it4.856
r_scbond_it3.299
r_mcangle_it1.916
r_angle_refined_deg1.542
r_mcbond_it1.126
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.318
r_dihedral_angle_3_deg15.88
r_dihedral_angle_1_deg6.597
r_dihedral_angle_4_deg5.097
r_scangle_it4.856
r_scbond_it3.299
r_mcangle_it1.916
r_angle_refined_deg1.542
r_mcbond_it1.126
r_chiral_restr0.122
r_bond_refined_d0.016
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1035
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms25

Software

Software
Software NamePurpose
XPREPdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
APEXdata collection
APEXdata reduction