2G8A

Lactobacillus casei Y261M in complex with substrate, dUMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7295Vapor diffusion against 20 mM KPO4 from protein solutions in the same buffer with 15-20 mM ammonium sulfate, DTT, and 38mM dUMP, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.9357.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.52α = 90
b = 78.52β = 90
c = 240.93γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATERIGAKU RAXIS IIC1996-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
12.439.3294.50.11712417124-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5587.23.42547

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.439.321712417124170494.50.2070.2030.2030.276RANDOM35.6
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]
-1.31-0.64-1.312.63
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.6
c_scangle_it4.71
c_scbond_it3.32
c_angle_deg2.6
c_mcangle_it2.51
c_improper_angle_d2.14
c_mcbond_it1.46
c_bond_d0.029
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.6
c_scangle_it4.71
c_scbond_it3.32
c_angle_deg2.6
c_mcangle_it2.51
c_improper_angle_d2.14
c_mcbond_it1.46
c_bond_d0.029
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 Atoms2589
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms20

Software

Software
Software NamePurpose
CNSrefinement
CCP4data scaling
CNSphasing