6XSE

Crystal structure of Staphylococcal nuclease variant Delta+PHS F34Y 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 DROP927726% MPD, 25 mM potassium phosphate, calcium chloride, THP
Crystal Properties
Matthews coefficientSolvent content
2.2344.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.958α = 90
b = 61.309β = 92.98
c = 38.051γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAGILENT ATLAS CCD2018-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER1.54

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
12.13899.90.02141.110.6836836.1
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)
12.12.181000.1435.776.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3BDC2.124.63793741799.940.23310.23060.2791RANDOM32.973
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]
-0.07-0.020.050.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.632
r_dihedral_angle_4_deg18.37
r_dihedral_angle_3_deg17.471
r_dihedral_angle_1_deg6.592
r_angle_refined_deg1.54
r_angle_other_deg1.338
r_chiral_restr0.055
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.632
r_dihedral_angle_4_deg18.37
r_dihedral_angle_3_deg17.471
r_dihedral_angle_1_deg6.592
r_angle_refined_deg1.54
r_angle_other_deg1.338
r_chiral_restr0.055
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1034
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
CrysalisProdata reduction
CrysalisProdata scaling