☰ Navigation Tabs
TPA bound-form of Periplasmic terephthalate binding protein (TBP) from Ideonella sakaiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 20 % PEG3350 and 0.2 M Ammonium iodide
Crystal Properties Matthews coefficient Solvent content 1.91 35.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.182 α = 90 b = 54.101 β = 104.55 c = 50.6 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2020-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.02 50 99.6 0.07 8.4 7 122150
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.02 1.04 99.9 0.744 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.02 20.67 115894 6204 99.41 0.20567 0.20441 0.2049 0.22927 0.2293 RANDOM 12.465
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] 0.6 -0.5 0.02 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.968 r_dihedral_angle_2_deg 7.727 r_dihedral_angle_1_deg 6.31 r_long_range_B_refined 4.553 r_long_range_B_other 4.259 r_scangle_other 3.049 r_scbond_it 2.031 r_scbond_other 2.028 r_angle_refined_deg 1.827 r_mcangle_it 1.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.968 r_dihedral_angle_2_deg 7.727 r_dihedral_angle_1_deg 6.31 r_long_range_B_refined 4.553 r_long_range_B_other 4.259 r_scangle_other 3.049 r_scbond_it 2.031 r_scbond_other 2.028 r_angle_refined_deg 1.827 r_mcangle_it 1.586 r_mcangle_other 1.577 r_mcbond_it 1.133 r_mcbond_other 1.121 r_angle_other_deg 0.615 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement HKL-2000 data reduction MOLREP phasing