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Crystal structure of Tyr p 36.0101
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 298 0.1 M citric acid pH 4.0, 0.8 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.04 39.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.974 α = 90 b = 54.974 β = 90 c = 79.315 γ = 120
Symmetry Space Group P 31 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 2022-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1.42 40 96.8 0.057 0.057 0.06 0.018 1 38.9 10 25963 -3
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 1.42 1.44 72.7 0.309 0.309 0.358 0.171 0.889 2.1 3.7
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 1.42 30.49 25922 1219 96.782 0.134 0.1331 0.1367 0.154 0.1568 15.173
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] 0.157 0.079 0.157 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.674 r_dihedral_angle_6_deg 15.24 r_dihedral_angle_3_deg 13.685 r_dihedral_angle_1_deg 6.533 r_rigid_bond_restr 3.732 r_lrange_other 2.452 r_lrange_it 2.436 r_scangle_it 1.707 r_scangle_other 1.706 r_angle_refined_deg 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.674 r_dihedral_angle_6_deg 15.24 r_dihedral_angle_3_deg 13.685 r_dihedral_angle_1_deg 6.533 r_rigid_bond_restr 3.732 r_lrange_other 2.452 r_lrange_it 2.436 r_scangle_it 1.707 r_scangle_other 1.706 r_angle_refined_deg 1.63 r_mcangle_other 1.427 r_mcangle_it 1.422 r_scbond_it 1.273 r_scbond_other 1.271 r_mcbond_it 0.985 r_mcbond_other 0.98 r_angle_other_deg 0.65 r_nbd_other 0.293 r_chiral_restr_other 0.262 r_nbd_refined 0.217 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.168 r_symmetry_nbd_refined 0.167 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.056 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 994 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing