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Crystal structure of TET25 in complex with PyDH2 ligand in P212121 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8G2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.05 M KCl, 0.1 M LiCl, 0.012 M spermine tetrahydrochloride, 0.05 M MES pH 6.5, 25% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.01 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.624 α = 90 b = 51.923 β = 90 c = 88.064 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 183 PIXEL DECTRIS PILATUS 6M-F 2023-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 1.62 25.96 98.4 0.103 0.999 8.8 12.8 8871
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 73.3 0.53 0.8 12.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.62 25.96 1.34 8843 487 99.9 0.2081 0.2068 0.2066 0.2279 0.2273 32.26
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 33.6535 f_angle_d 1.3109 f_chiral_restr 0.0633 f_bond_d 0.0121 f_plane_restr 0.0112
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1062 Solvent Atoms 18 Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement PHENIX phasing XDS data reduction XDS data scaling Coot model building