5D42

2009 H1N1 PA endonuclease mutant F105S in complex with dTMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5D2OPDB entry 5D2O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52910.2 M magnesium chloride, 2 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.3647.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.084α = 90
b = 74.084β = 90
c = 130.312γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2015-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
125098.70.0670.0690.01811.81414714
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0792.10.8930.9310.2550.75911.61330

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 5D2O2501393176198.420.18520.18240.2369RANDOM47.191
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]
-0.91-0.46-0.912.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.032
r_dihedral_angle_4_deg16.787
r_dihedral_angle_3_deg15.753
r_dihedral_angle_1_deg6.539
r_mcangle_it3.873
r_mcbond_it2.801
r_mcbond_other2.798
r_angle_refined_deg2.218
r_angle_other_deg1.163
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.032
r_dihedral_angle_4_deg16.787
r_dihedral_angle_3_deg15.753
r_dihedral_angle_1_deg6.539
r_mcangle_it3.873
r_mcbond_it2.801
r_mcbond_other2.798
r_angle_refined_deg2.218
r_angle_other_deg1.163
r_chiral_restr0.125
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1438
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms23

Software

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