3E76

Crystal structure of Wild-type GroEL with bound Thallium ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XCKPDB Entry: 1XCK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2762.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.676α = 90
b = 260.954β = 90
c = 287.872γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97741NSLSX4A

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
13.9450980.18912.88.390513-3
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)
13.944.08880.962.15.2

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 REPLACEMENTTHROUGHOUTPDB Entry: 1XCK3.9449.3984364445697.70.2620.2610.293RANDOM125.21
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]
-3.53-1.485.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.542
r_dihedral_angle_3_deg16.526
r_dihedral_angle_4_deg14.587
r_dihedral_angle_1_deg4.16
r_angle_refined_deg0.919
r_symmetry_vdw_refined0.322
r_nbtor_refined0.285
r_symmetry_hbond_refined0.231
r_nbd_refined0.181
r_metal_ion_refined0.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.542
r_dihedral_angle_3_deg16.526
r_dihedral_angle_4_deg14.587
r_dihedral_angle_1_deg4.16
r_angle_refined_deg0.919
r_symmetry_vdw_refined0.322
r_nbtor_refined0.285
r_symmetry_hbond_refined0.231
r_nbd_refined0.181
r_metal_ion_refined0.181
r_xyhbond_nbd_refined0.133
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms53970
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms494

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing