4WRD

Crystal structure of Staphylcoccal nulease variant Delta+PHS V66E L125E at cryogenic temperature


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BDC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627720% MPD, 25mM potassium phosphate, calcium chloride, pdTp
Crystal Properties
Matthews coefficientSolvent content
2.2244.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.14α = 90
b = 60.315β = 94.05
c = 38.364γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAPEX II CCDmulti-layer optics2014-08-04MSINGLE 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
11.6538.2799.90.01142.6827.81171551715524.6
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)
11.651.6797.60.13986.638.71

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 REPLACEMENTTHROUGHOUT3BDC1.6538.271623986499.680.18420.18230.22RANDOM20.713
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]
-1.020.53-1.061.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.449
r_dihedral_angle_3_deg12.889
r_dihedral_angle_4_deg10.214
r_dihedral_angle_1_deg6.587
r_mcangle_it2.752
r_mcbond_it1.987
r_mcbond_other1.95
r_angle_refined_deg1.62
r_angle_other_deg0.741
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.449
r_dihedral_angle_3_deg12.889
r_dihedral_angle_4_deg10.214
r_dihedral_angle_1_deg6.587
r_mcangle_it2.752
r_mcbond_it1.987
r_mcbond_other1.95
r_angle_refined_deg1.62
r_angle_other_deg0.741
r_chiral_restr0.103
r_bond_refined_d0.017
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1036
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms26

Software

Software
Software NamePurpose
SAINTdata scaling
SAINTdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction