3LIE

Crystal Structure of the extracellular domain of the putative histidine kinase vpHK1S-Z8


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72932M NaCl, 0.2M MgCl, 0.1M Tris, pH 7.0, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2846.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.049α = 90
b = 114.953β = 90
c = 69.624γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97921NSLSX4A

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
12.65097.70.07714.24.219533
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)
2.62.6995.90.3554.11882

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.5939.0281950199197.180.2580.2540.326RANDOM57.454
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]
0.340.32-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.812
r_dihedral_angle_3_deg18.978
r_dihedral_angle_4_deg18.048
r_dihedral_angle_1_deg7.268
r_scangle_it3.022
r_scbond_it1.831
r_angle_refined_deg1.708
r_mcangle_it1.359
r_mcbond_it0.724
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.812
r_dihedral_angle_3_deg18.978
r_dihedral_angle_4_deg18.048
r_dihedral_angle_1_deg7.268
r_scangle_it3.022
r_scbond_it1.831
r_angle_refined_deg1.708
r_mcangle_it1.359
r_mcbond_it0.724
r_chiral_restr0.103
r_bond_refined_d0.017
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4285
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms2

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction