3SHL

Crystal structure of Staphylococcal nuclease variant Delta+PHS V74KL25A 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 DROP827730% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2445

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.2α = 90
b = 60.449β = 90
c = 74.142γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

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
11.4750990.05915.413.3248622486225.1
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)
11.471.599.40.37413.51212

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3BDC1.4829.532481624816251498.920.18920.18610.2164RANDOM20.9597
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]
0.21-0.860.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.897
r_dihedral_angle_3_deg15.949
r_dihedral_angle_4_deg12.035
r_dihedral_angle_1_deg6.911
r_scangle_it4.855
r_scbond_it3.223
r_mcangle_it1.905
r_angle_refined_deg1.615
r_mcbond_it1.22
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.897
r_dihedral_angle_3_deg15.949
r_dihedral_angle_4_deg12.035
r_dihedral_angle_1_deg6.911
r_scangle_it4.855
r_scbond_it3.223
r_mcangle_it1.905
r_angle_refined_deg1.615
r_mcbond_it1.22
r_chiral_restr0.126
r_gen_planes_refined0.015
r_bond_refined_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1032
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms26

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction