8HKB

TPA bound-form of Periplasmic terephthalate binding protein (TBP) from Ideonella sakaiensis mutant K184D


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NDR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1525 % PEG3350 and 0.2 M Ammonium citrate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
1.9336.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.054α = 90
b = 59.302β = 104.27
c = 54.298γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702021-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

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
11.450990.07815.91.748172
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)
11.41.4298.50.6881.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.428.1245754240398.790.154130.152730.18061RANDOM13.329
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]
0.05-0.430.61-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.67
r_dihedral_angle_2_deg11.034
r_dihedral_angle_1_deg6.438
r_long_range_B_refined5.193
r_long_range_B_other4.928
r_scangle_other3.842
r_scbond_other2.621
r_scbond_it2.617
r_mcangle_it2.238
r_mcangle_other2.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.67
r_dihedral_angle_2_deg11.034
r_dihedral_angle_1_deg6.438
r_long_range_B_refined5.193
r_long_range_B_other4.928
r_scangle_other3.842
r_scbond_other2.621
r_scbond_it2.617
r_mcangle_it2.238
r_mcangle_other2.238
r_angle_refined_deg1.876
r_mcbond_it1.469
r_mcbond_other1.469
r_angle_other_deg0.604
r_chiral_restr0.102
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2281
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms12

Software

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