3NP8

Crystal structure of Staphylococcal nuclease variant Delta+PHS L36A at cryogenic temperature


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BDC3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, L36A, Q30A, K64A, T82A, Y113A, V114A, Y115A; all b-factors were reset to 20 A^2.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627720% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 6.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2244.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.011α = 90
b = 60.404β = 93.77
c = 38.275γ = 90
Symmetry
Space GroupP 1 21 1

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 X251.1000NSLSX25

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
11.75098.90.0421.97.1154631546336.9
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)
11.71.7392.60.2536.1736

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, L36A, Q30A, K64A, T82A, Y113A, V114A, Y115A; all b-factors were reset to 20 A^2.1.730.9415410154098.950.18940.19330.18940.2296RANDOM34.2096
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]
-1.50.7-1.322.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.862
r_dihedral_angle_3_deg18.194
r_dihedral_angle_4_deg6.858
r_dihedral_angle_1_deg6.589
r_scangle_it4.43
r_scbond_it3.332
r_mcangle_it1.977
r_angle_refined_deg1.677
r_mcbond_it1.353
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.862
r_dihedral_angle_3_deg18.194
r_dihedral_angle_4_deg6.858
r_dihedral_angle_1_deg6.589
r_scangle_it4.43
r_scbond_it3.332
r_mcangle_it1.977
r_angle_refined_deg1.677
r_mcbond_it1.353
r_chiral_restr0.128
r_bond_refined_d0.017
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1030
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms26

Software

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