5KGU

Crystal structure of Staphylococcal nuclease variant Delta+PHS N118D 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 DROP727725% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties
Matthews coefficientSolvent content
2.2344.81

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 CCD2016-05-09MSINGLE 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
11.95099.90.01756.5510.41110929.15
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)
11.91.971000.1046.877.1

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 3BDC1.938.351050459097.940.17760.17470.233RANDOM28.278
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]
-2.190.3-1.223.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.979
r_dihedral_angle_3_deg18.136
r_dihedral_angle_4_deg10.553
r_dihedral_angle_1_deg7.067
r_angle_refined_deg1.88
r_mcangle_it1.713
r_mcbond_it1.218
r_mcbond_other1.203
r_angle_other_deg0.894
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.979
r_dihedral_angle_3_deg18.136
r_dihedral_angle_4_deg10.553
r_dihedral_angle_1_deg7.067
r_angle_refined_deg1.88
r_mcangle_it1.713
r_mcbond_it1.218
r_mcbond_other1.203
r_angle_other_deg0.894
r_chiral_restr0.119
r_bond_refined_d0.017
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 Atoms1033
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms26

Software

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