3UKJ

Crystal structure of extracellular ligand-binding receptor from Rhodopseudomonas palustris HaA2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529710 mM Nickel chloride, 0.1M Tris, 20% PEG2000 MME, 10 mM Praseodymium Acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
238.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.685α = 90
b = 70.314β = 90
c = 104.688γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97921APS19-ID

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
11.65098.80.09831.96.54259742082-3
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)
11.61.6397.50.5892.465.62037

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 DIFFRACTIONSADTHROUGHOUT1.6504203242032212798.810.16090.16090.15850.2056RANDOM18.1433
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]
-1.972.2-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.204
r_dihedral_angle_4_deg18.717
r_dihedral_angle_3_deg11.77
r_dihedral_angle_1_deg5.345
r_scangle_it4.69
r_scbond_it3.252
r_mcangle_it1.947
r_rigid_bond_restr1.536
r_angle_refined_deg1.43
r_mcbond_it1.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.204
r_dihedral_angle_4_deg18.717
r_dihedral_angle_3_deg11.77
r_dihedral_angle_1_deg5.345
r_scangle_it4.69
r_scbond_it3.252
r_mcangle_it1.947
r_rigid_bond_restr1.536
r_angle_refined_deg1.43
r_mcbond_it1.249
r_chiral_restr0.119
r_gen_planes_refined0.021
r_bond_refined_d0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2689
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building