5D8U

2009 H1N1 PA endonuclease mutant E119D in complex with L-742,001


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 sodium, pH 7.5, 1.0 M ammonium sulfate, 2% w/v PEG400, 50 mM magnesium chloride, 50 mM manganese chloride
Crystal Properties
Matthews coefficientSolvent content
2.9357.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.881α = 90
b = 89.881β = 90
c = 134.148γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2014-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97921APS22-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
12.295099.60.0620.0640.01810.812.412715
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)
12.292.3795.90.8190.8640.2670.7929.61219

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 5CZN2.29461209162299.550.20030.19820.2408RANDOM65.79
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]
1.061.06-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.759
r_dihedral_angle_3_deg17.981
r_dihedral_angle_4_deg16.89
r_dihedral_angle_1_deg7.901
r_mcangle_it4.83
r_mcbond_it3.199
r_mcbond_other3.183
r_angle_refined_deg2.371
r_angle_other_deg1.246
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.759
r_dihedral_angle_3_deg17.981
r_dihedral_angle_4_deg16.89
r_dihedral_angle_1_deg7.901
r_mcangle_it4.83
r_mcbond_it3.199
r_mcbond_other3.183
r_angle_refined_deg2.371
r_angle_other_deg1.246
r_chiral_restr0.133
r_bond_refined_d0.026
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1403
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms24

Software

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