5IGC

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23E/V66H 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 DROP627720% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties
Matthews coefficientSolvent content
2.2344.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.1α = 90
b = 60.592β = 93.97
c = 38.547γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAGILENT ATLAS CCD2015-09-22MSINGLE 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
11.85099.90.01951.0910.11331825.8
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)
11.81.871000.1236.246.8

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 3BDC1.838.451264865499.950.19120.18930.2253RANDOM21.929
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.827
r_dihedral_angle_3_deg15.625
r_dihedral_angle_4_deg10.621
r_dihedral_angle_1_deg6.47
r_mcangle_it2.824
r_mcbond_it1.996
r_mcbond_other1.976
r_angle_refined_deg1.835
r_angle_other_deg0.959
r_chiral_restr0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.827
r_dihedral_angle_3_deg15.625
r_dihedral_angle_4_deg10.621
r_dihedral_angle_1_deg6.47
r_mcangle_it2.824
r_mcbond_it1.996
r_mcbond_other1.976
r_angle_refined_deg1.835
r_angle_other_deg0.959
r_chiral_restr0.108
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1038
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms26

Software

Software
Software NamePurpose
XPREPdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction