7K4W

Crystal structure of Kemp Eliminase HG3.17 in the inactive state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BS0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP310The protein was dialyzed in 380 mM Bis-Tris propane, pH 10, and 200 mM calcium chloride. Crystals were obtained in 2.1 M malic acid, pH 7.
Crystal Properties
Matthews coefficientSolvent content
2.3247.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.39α = 90
b = 67.39β = 90
c = 74.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.950.0499.820.9794.7411.92503320.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9680.251

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4bs01.950.041.3325011376199.630.21360.21010.254625.04
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_d6.1054
f_angle_d0.9206
f_chiral_restr0.05
f_bond_d0.0081
f_plane_restr0.0081
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2171
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms1

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing