6ZPC

Cyanophage S-2L HD phosphohydrolase (DatZ) bound to dATP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291.151.5 M LiSO4; 100 mM HEPES; 10 mM EDTA
Crystal Properties
Matthews coefficientSolvent content
2.5251.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.65α = 90
b = 141.65β = 90
c = 53.73γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9MKB Mirrors2019-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.980100SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.2683593520640.8999.80.0660.0680.015121.519.55425015.8895422676
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)
11.268359352061.397.71.2871.3260.3120.686217.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE1.2683593520640.41609124251.3865467029454217271199.77181133950.1268287456940.1258146102080.14608110934722.5874180448
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.9793375773
f_angle_d1.0335119658
f_chiral_restr0.0677262197426
f_bond_d0.00771259674338
f_plane_restr0.00731991570705
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1395
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms33

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing