2FKW

Structure of LH2 from Rps. acidophila crystallized in lipidic mesophases


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NKZPDB entry 1NKZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18293200 microlitres of 40 %(w/w) protein, 0.05 %(w/v) LDAO, 20mM Tris/HCl and 60 %(w/w) monoolein mixed with 2 microlitres of precipitant: 20 %(w/v) pentaerythritol propoxylate, 0.1 M potassium formate, 0.1 M Tris/HCl, pH 8.0, Mesophase crystallization, lipidic cubic phase, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6165.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.443α = 90
b = 126.384β = 90
c = 129.705γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.9124CHESSF1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.44990.53699.80.06620.93.94999949795
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.5498.250.5682.33.73208

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1NKZ2.45104999948989249899.780.186510.182820.25367RANDOM41.842
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]
2.97-4.141.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.173
r_dihedral_angle_3_deg18.044
r_dihedral_angle_4_deg10.639
r_dihedral_angle_1_deg8.963
r_scangle_it4.217
r_scbond_it2.866
r_mcangle_it2.016
r_angle_refined_deg1.414
r_mcbond_it1.26
r_angle_other_deg0.849
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.173
r_dihedral_angle_3_deg18.044
r_dihedral_angle_4_deg10.639
r_dihedral_angle_1_deg8.963
r_scangle_it4.217
r_scbond_it2.866
r_mcangle_it2.016
r_angle_refined_deg1.414
r_mcbond_it1.26
r_angle_other_deg0.849
r_chiral_restr0.784
r_metal_ion_refined0.382
r_xyhbond_nbd_refined0.353
r_nbd_refined0.334
r_symmetry_hbond_refined0.325
r_mcbond_other0.319
r_nbd_other0.247
r_symmetry_vdw_refined0.232
r_nbtor_refined0.195
r_symmetry_vdw_other0.175
r_nbtor_other0.101
r_bond_refined_d0.03
r_gen_planes_other0.019
r_gen_planes_refined0.015
r_bond_other_d0.005
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6534
Nucleic Acid Atoms
Solvent Atoms613
Heterogen Atoms2682

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing