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Crystal structure of Tyr p 36.0101 in complex with a poly(L-proline) peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TI5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 298 0.1 M lithium citrate pH 3.5, 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.15 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.289 α = 90 b = 55.518 β = 121.179 c = 59.032 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER X 16M 2023-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 2.05 40 91.4 0.075 0.075 0.082 0.033 0.989 16.6 5.4 13911
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 65.1 0.214 0.214 0.267 0.157 0.932 2.5 2.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.059 37.768 13909 695 91.057 0.171 0.1687 0.1775 0.2153 0.2206 21.047
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] 0.061 -0.092 0.223 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.06 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_2_deg 7.516 r_dihedral_angle_1_deg 6.697 r_lrange_it 6.302 r_lrange_other 6.122 r_scangle_it 4.033 r_scangle_other 3.992 r_scbond_it 2.564 r_mcangle_other 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.06 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_2_deg 7.516 r_dihedral_angle_1_deg 6.697 r_lrange_it 6.302 r_lrange_other 6.122 r_scangle_it 4.033 r_scangle_other 3.992 r_scbond_it 2.564 r_mcangle_other 2.49 r_mcangle_it 2.489 r_scbond_other 2.488 r_mcbond_it 1.575 r_mcbond_other 1.575 r_angle_refined_deg 1.483 r_angle_other_deg 0.497 r_nbd_other 0.235 r_nbd_refined 0.207 r_symmetry_nbd_other 0.207 r_symmetry_xyhbond_nbd_refined 0.2 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.171 r_ncsr_local_group_1 0.151 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.069 r_chiral_restr_other 0.022 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2040 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing