5DEB

2009 H1N1 PA endonuclease mutant E119D in complex with rUMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CZNPDB entry 5CZN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52910.1 M HEPES, pH 7.5, 1.0 M ammonium sulfate, 2% w/v PEG400, 50 mM magnesium chloride, 50 mM manganese chloride, 200 mM rUMP
Crystal Properties
Matthews coefficientSolvent content
2.9458.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.057α = 90
b = 90.057β = 90
c = 134.337γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00522APS22-ID

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
12.075099.70.06636.8211.917236
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.149910.2

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 5CZN2.1446.211476483599.740.20830.2060.2487RANDOM68.585
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]
0.970.97-1.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_4_deg16.453
r_dihedral_angle_3_deg15.418
r_dihedral_angle_1_deg6.734
r_mcangle_it3.267
r_mcbond_other2.069
r_mcbond_it2.068
r_angle_refined_deg1.741
r_angle_other_deg1.045
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_4_deg16.453
r_dihedral_angle_3_deg15.418
r_dihedral_angle_1_deg6.734
r_mcangle_it3.267
r_mcbond_other2.069
r_mcbond_it2.068
r_angle_refined_deg1.741
r_angle_other_deg1.045
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1428
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms23

Software

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