4PMB

Crystal structure of Staphylcoccal nuclease variant Delta+PHS I92S 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 DROP827725% MPD, 25mM potassium phosphate, calcium chloride, pdTp
Crystal Properties
Matthews coefficientSolvent content
2.1943.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.031α = 90
b = 59.964β = 93.63
c = 38.017γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAPEX II CCDmirrors2013-05-07MSINGLE 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
11.859.9699.90.034718.959.08129781297827.2
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)
11.81.831000.22665.68

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 3BDC1.837.941295063099.810.19790.19640.2269RANDOM22.129
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]
-0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.432
r_dihedral_angle_3_deg15.243
r_dihedral_angle_4_deg7.998
r_dihedral_angle_1_deg6.486
r_angle_refined_deg1.823
r_angle_other_deg0.806
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.432
r_dihedral_angle_3_deg15.243
r_dihedral_angle_4_deg7.998
r_dihedral_angle_1_deg6.486
r_angle_refined_deg1.823
r_angle_other_deg0.806
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1031
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms26

Software

Software
Software NamePurpose
SAINTdata reduction
SAINTdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction