3TX6

The Structure of a putative ABC-transporter periplasmic component from Rhodopseudomonas palustris


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72970.1M Bis-Tris Propane:NaOH pH 7.0, 2.5M Amonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
1.9336.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.564α = 90
b = 68.668β = 90
c = 90.779γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-04-18MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97921, 0.97935APS19-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
11.55099.80.07510.88.64922449224-318.7
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)
11.51.5399.90.4597.92464

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 DIFFRACTIONMADTHROUGHOUT1.5504903449034248399.380.140.140.1370.1981RANDOM24.7198
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]
-0.340.30.04
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.23
r_dihedral_angle_2_deg33.208
r_sphericity_bonded16.176
r_dihedral_angle_4_deg13.642
r_dihedral_angle_3_deg13.547
r_dihedral_angle_1_deg5.775
r_rigid_bond_restr4.1
r_angle_refined_deg1.696
r_angle_other_deg0.997
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free42.23
r_dihedral_angle_2_deg33.208
r_sphericity_bonded16.176
r_dihedral_angle_4_deg13.642
r_dihedral_angle_3_deg13.547
r_dihedral_angle_1_deg5.775
r_rigid_bond_restr4.1
r_angle_refined_deg1.696
r_angle_other_deg0.997
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2703
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms32

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building