3LR3

Periplasmic domain of the risS sensor protein from Burkholderia pesuromallei, low pH native structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LR0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5289JCSG+ condition A6, 0.1 M phosphate-citrate pH 4.2, 0.2 M lithium sulfate, 25% PEG 1000, crystal tracking ID 208087a6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3146.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.883α = 90
b = 58.883β = 90
c = 75.973γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.97650ALS5.0.3

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
12.130.4698.50.0713.213.79199
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)
12.12.1887.10.3753.255.4816

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT3LR02.130.46917543998.410.1830.1810.223RANDOM25.214
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]
0.380.190.38-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.015
r_dihedral_angle_4_deg21.242
r_dihedral_angle_3_deg13.237
r_dihedral_angle_1_deg6.244
r_scangle_it4.109
r_scbond_it2.373
r_mcangle_it1.459
r_angle_refined_deg1.355
r_mcbond_it0.79
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.015
r_dihedral_angle_4_deg21.242
r_dihedral_angle_3_deg13.237
r_dihedral_angle_1_deg6.244
r_scangle_it4.109
r_scbond_it2.373
r_mcangle_it1.459
r_angle_refined_deg1.355
r_mcbond_it0.79
r_chiral_restr0.089
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms911
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling