☰ Navigation Tabs
Crystal structure of TphC in an open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Morpheus B5 - 0.09M Halogens (0.3M Sodium fluoride; 0.3M Sodium
bromide; 0.3M Sodium iodide) 0.1M Buffer System 2 pH 7.5 (1.0M 7.5 Sodium HEPES; MOPS (acid) ) 30% v/v precipitant mix 1 (40% v/v PEG 500* MME; 20
% w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.113 α = 90 b = 81.269 β = 109.547 c = 186.953 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 PILATUS3 6M 2020-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.88 70.48 99.41 0.2251 0.2438 0.0927 0.992 6.9 6.9 161975 26.13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.947 95.4 2.175 2.35 0.88 0.838 0.56 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4X9T 1.97 70.48 1.35 140722 7252 99.88 0.1842 0.1822 0.1831 0.2215 0.2217 29.21
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.1474 f_angle_d 0.8946 f_chiral_restr 0.0631 f_bond_d 0.0131 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13259 Nucleic Acid Atoms Solvent Atoms 1649 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing