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Crystal structure of TCPTP catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.15 M Ammonium nitrate, 0.1 M MES (pH-6.0), 20% v/v PEG smear medium, 5% v/v Ethylene glycol and 5.5 mM lysine dipeptide additive
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.57 α = 112.932 b = 68.056 β = 106.459 c = 73.244 γ = 92.459
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 107 CCD RAYONIX MX300HE 2019-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.93 20 92 0.017 0.99 41.6 2.2 63299
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2 96.3 0.083 0.98 9.7 2.2
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 1L8K 1.93 19.948 62827 3120 91.178 0.186 0.1834 0.192 0.2376 0.2426 24.787
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] -0.153 0.09 0.072 -0.064 0.017 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 21.1 r_dihedral_angle_3_deg 18.566 r_dihedral_angle_1_deg 6.903 r_lrange_it 6.024 r_lrange_other 5.966 r_scangle_it 4.225 r_scangle_other 4.224 r_mcangle_it 3.296 r_mcangle_other 3.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.822 r_dihedral_angle_4_deg 21.1 r_dihedral_angle_3_deg 18.566 r_dihedral_angle_1_deg 6.903 r_lrange_it 6.024 r_lrange_other 5.966 r_scangle_it 4.225 r_scangle_other 4.224 r_mcangle_it 3.296 r_mcangle_other 3.296 r_scbond_it 2.649 r_scbond_other 2.648 r_mcbond_it 2.202 r_mcbond_other 2.2 r_angle_refined_deg 1.616 r_angle_other_deg 1.353 r_nbd_other 0.276 r_symmetry_nbd_refined 0.247 r_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.167 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.085 r_symmetry_xyhbond_nbd_other 0.045 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7191 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing