4H9U

Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting-drop vapor diffusion7.5293100 mM Tris, pH 7.5, 20% (w/v) PEG 4000, 10% (v/v) glycerol, 0.1 mM ZnCl2, sitting-drop vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.34α = 90
b = 157.122β = 116.18
c = 49.936γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.000NSRRCBL13B1

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
12.09930980.06214.23.63742737427
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1492.50.41831786

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2.09919.8893381233812169588.720.17470.17470.17250.2168random32.5037
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]
4.48450.12370.6511.3652
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.752
f_angle_d1.288
f_chiral_restr0.084
f_bond_d0.012
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5086
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms6

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
DENZOdata reduction