3WDM

Crystal structure of 4-phosphopantoate-beta-alanine ligase from Thermococcus kodakarensis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529318-20% PEG 3350, 200mM ammonium acetate, 100mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1342.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.802α = 90
b = 80.814β = 110.07
c = 84.225γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2012-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.1Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125097.2669566695618
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0395.6

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUT235.9935797829130.2180.2180.269RANDOM39.7
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]
-3.987.5110.27-6.28
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.9
c_scangle_it2.96
c_mcangle_it2.07
c_scbond_it2.05
c_mcbond_it1.38
c_angle_deg1.3
c_improper_angle_d0.88
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.9
c_scangle_it2.96
c_mcangle_it2.07
c_scbond_it2.05
c_mcbond_it1.38
c_angle_deg1.3
c_improper_angle_d0.88
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7909
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms76

Software

Software
Software NamePurpose
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling