4IAL

Crystal structure of Staphylococcal nuclease variant Delta+PHS H121E 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 DROP827724% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2344.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.03α = 90
b = 60.395β = 92.32
c = 38.387γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMeridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification2012-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.10NSLSX25

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
11.59538.35597.70.05138.3323.7184391843934.5
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)
11.5951.6385.90.2614.012.8825

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3BDC1.59538.355184301843094497.370.19890.19890.19680.2389RANDOM35.6892
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]
-3.740.45-0.984.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.275
r_dihedral_angle_4_deg18.783
r_dihedral_angle_3_deg14.853
r_dihedral_angle_1_deg6.78
r_angle_refined_deg1.908
r_angle_other_deg0.84
r_chiral_restr0.124
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.275
r_dihedral_angle_4_deg18.783
r_dihedral_angle_3_deg14.853
r_dihedral_angle_1_deg6.78
r_angle_refined_deg1.908
r_angle_other_deg0.84
r_chiral_restr0.124
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1032
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms26

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
DENZOdata reduction