5C3X

Crystal structure of Staphylococcal nuclease variant Delta+PHS I72D/N100E 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 DROP627730% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.126α = 90
b = 60.173β = 95.03
c = 38.047γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAPEX II CCDmirrors2014-01-16MSINGLE 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
11.95501000.020336.0623.95102711027130.35
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)
11.951.981000.11877.8917.57

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 3BDC1.9537.997664941000.16830.16620.2077RANDOM26.141
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]
-1.160.11-0.091.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.714
r_dihedral_angle_3_deg17.427
r_dihedral_angle_1_deg6.526
r_dihedral_angle_4_deg5.685
r_angle_refined_deg1.877
r_mcangle_it1.527
r_mcbond_it0.989
r_mcbond_other0.975
r_angle_other_deg0.806
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.714
r_dihedral_angle_3_deg17.427
r_dihedral_angle_1_deg6.526
r_dihedral_angle_4_deg5.685
r_angle_refined_deg1.877
r_mcangle_it1.527
r_mcbond_it0.989
r_mcbond_other0.975
r_angle_other_deg0.806
r_chiral_restr0.106
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1034
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms26

Software

Software
Software NamePurpose
SAINTdata scaling
APEXdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
SAINTdata reduction