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Crystal Structure of TPP1 K170del
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 3.6 M sodium formate, 100 mM Tris-Cl pH 8.0
Crystal Properties Matthews coefficient Solvent content 4.34 71.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.026 α = 90 b = 119.026 β = 90 c = 170.778 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 2014-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.03829 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3 50 99.7 0.148 0.16 0.059 7.1 6.9 12617
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 3 3.11 100 0.485 7
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 (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 2I46 3 50 11321 1281 99.68 0.1954 0.192 0.192 0.2256 0.2256 RANDOM 37.111
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] 0.99 0.99 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.58 r_dihedral_angle_4_deg 17.334 r_dihedral_angle_3_deg 16.636 r_dihedral_angle_1_deg 5.321 r_mcangle_it 3.939 r_mcbond_it 2.117 r_scbond_it 1.714 r_angle_refined_deg 0.988 r_chiral_restr 0.059 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.58 r_dihedral_angle_4_deg 17.334 r_dihedral_angle_3_deg 16.636 r_dihedral_angle_1_deg 5.321 r_mcangle_it 3.939 r_mcbond_it 2.117 r_scbond_it 1.714 r_angle_refined_deg 0.988 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2178 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing