5D9J

2009 H1N1 PA endonuclease mutant F105S in complex with L-742,001


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E5EPDB entry 4E5E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72910.8 M succinic acid, pH 7.0, 5 mM magnesium chloride, 5 mM manganese chloride
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.585α = 90
b = 60.585β = 90
c = 95.98γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2014-08-09MSINGLE 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
11.85401000.0630.0650.01510.318.817865
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)
11.851.921000.8830.9120.2260.88915.71764

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 4E5E1.8535.411687196099.820.18510.18260.2295RANDOM42.079
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]
0.060.030.06-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_4_deg17.892
r_dihedral_angle_3_deg15.554
r_dihedral_angle_1_deg6.395
r_mcangle_it3.298
r_angle_refined_deg2.615
r_mcbond_it2.362
r_mcbond_other2.359
r_angle_other_deg1.288
r_chiral_restr0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_4_deg17.892
r_dihedral_angle_3_deg15.554
r_dihedral_angle_1_deg6.395
r_mcangle_it3.298
r_angle_refined_deg2.615
r_mcbond_it2.362
r_mcbond_other2.359
r_angle_other_deg1.288
r_chiral_restr0.17
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1413
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms24

Software

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