5I6W

Crystal structure of Staphylococcal nuclease variant Delta+PHS A58D 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 DROP827718% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties
Matthews coefficientSolvent content
2.2344.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.178α = 90
b = 60.353β = 93.52
c = 38.425γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAGILENT ATLAS CCD2016-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER1.5418

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
11.9501000.01854.1710.51123526.93
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)
11.91.971000.1057.177.3

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 3BDC1.938.351062259898.20.18420.18140.2355RANDOM26.866
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]
-2.290.57-2.534.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.528
r_dihedral_angle_3_deg17.305
r_dihedral_angle_4_deg9.41
r_dihedral_angle_1_deg7.276
r_mcangle_it2.079
r_angle_refined_deg1.792
r_mcbond_it1.318
r_mcbond_other1.3
r_angle_other_deg0.868
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.528
r_dihedral_angle_3_deg17.305
r_dihedral_angle_4_deg9.41
r_dihedral_angle_1_deg7.276
r_mcangle_it2.079
r_angle_refined_deg1.792
r_mcbond_it1.318
r_mcbond_other1.3
r_angle_other_deg0.868
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1036
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
CrysalisProdata reduction
Cootmodel building