8HK9

Apo-form of Periplasmic terephthalate binding protein (TBP) from Ideonella sakaiensis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1520 % PEG3350 and 0.2 M Magnesium nitrate hexahydrate
Crystal Properties
Matthews coefficientSolvent content
2.5251.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.883α = 90
b = 131.883β = 90
c = 75.577γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702020-11-13MSINGLE 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
125090.40.06214.51.843351
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)
122.0383.80.2591.6

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 REPLACEMENTTHROUGHOUT232.9941131222098.270.183990.180990.23749RANDOM34.164
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]
-1.14-1.142.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.216
r_dihedral_angle_2_deg8.681
r_long_range_B_refined6.822
r_dihedral_angle_1_deg6.785
r_long_range_B_other6.761
r_scangle_other5.235
r_mcangle_it4.042
r_mcangle_other4.042
r_scbond_it3.482
r_scbond_other3.481
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.216
r_dihedral_angle_2_deg8.681
r_long_range_B_refined6.822
r_dihedral_angle_1_deg6.785
r_long_range_B_other6.761
r_scangle_other5.235
r_mcangle_it4.042
r_mcangle_other4.042
r_scbond_it3.482
r_scbond_other3.481
r_mcbond_it2.945
r_mcbond_other2.938
r_angle_refined_deg1.412
r_angle_other_deg0.439
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.007
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 Atoms4392
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms

Software

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