4MIU

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23T/V99T 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 DROP927720% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2344.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.204α = 90
b = 60.554β = 93.32
c = 38.201γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAPEX II CCDMultilayer2013-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER1.54

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
11.67501000.01546.511.7165551655529.9
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)
11.671.771000.1845.18.32612

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 3BDC1.6738.14165281652883599.930.18660.18660.18410.2347RANDOM24.0906
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]
-1.080.26-1.132.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.934
r_dihedral_angle_3_deg14.628
r_dihedral_angle_4_deg9.602
r_dihedral_angle_1_deg6.073
r_angle_refined_deg1.907
r_chiral_restr0.135
r_bond_refined_d0.019
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1033
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms26

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
APEXdata collection
APEXdata reduction