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Crystal structure of TPADO in complex with 2-OH-TPA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N0Q 3N0Q, 3EBY experimental model PDB 3EBY 3N0Q, 3EBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 12.5% MPD,
12.5% PEG 3350,
12.5% PEG 1000,
0.3 M sodium nitrate,
0.3 M sodium phosphate dibasic,
0.3 M ammonium sulfate,
0.1 M buffer Imidazole/MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.85 56.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.312 α = 90 b = 220.312 β = 90 c = 83.175 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2021-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.948 190.796 96.4 0.109 0.027 0.999 17.9 17.3 149913
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.948 2.057 57.4 2.372 0.56 0.59 1.4 18.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3N0Q, 3EBY 1.95 190.796 149903 7226 89.47 0.167 0.1648 0.1633 0.2022 0.2005 43.123
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] 0.027 0.014 0.027 -0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.374 r_dihedral_angle_4_deg 17.993 r_dihedral_angle_3_deg 14.079 r_dihedral_angle_1_deg 7.482 r_lrange_it 7.052 r_lrange_other 7.046 r_scangle_other 5.378 r_scangle_it 5.377 r_mcangle_it 3.94 r_mcangle_other 3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.374 r_dihedral_angle_4_deg 17.993 r_dihedral_angle_3_deg 14.079 r_dihedral_angle_1_deg 7.482 r_lrange_it 7.052 r_lrange_other 7.046 r_scangle_other 5.378 r_scangle_it 5.377 r_mcangle_it 3.94 r_mcangle_other 3.94 r_scbond_it 3.776 r_scbond_other 3.772 r_mcbond_it 2.835 r_mcbond_other 2.835 r_angle_refined_deg 1.814 r_angle_other_deg 1.449 r_nbd_other 0.243 r_symmetry_nbd_refined 0.235 r_symmetry_xyhbond_nbd_other 0.206 r_nbd_refined 0.201 r_symmetry_nbd_other 0.184 r_symmetry_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.152 r_ncsr_local_group_4 0.103 r_ncsr_local_group_2 0.1 r_ncsr_local_group_6 0.099 r_ncsr_local_group_1 0.098 r_ncsr_local_group_5 0.087 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_3 0.079 r_bond_refined_d 0.014 r_xyhbond_nbd_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13861 Nucleic Acid Atoms Solvent Atoms 921 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing