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X-ray crystal structure of TEBP-1 MCD2 homodimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 TEBP-1 MCD2 + 1 M succinic acid, 9 mM cobalt chloride, 100 mM HEPES, pH 7.5, 16 degrees C, hanging drop, cryoprotectant: 1.2 M succinic acid, 7 mM cobalt chloride, 100 mM HEPES, pH 7.2
Crystal Properties Matthews coefficient Solvent content 3.13 60.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.842 α = 90 b = 59.965 β = 101.823 c = 151.966 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 CCD RAYONIX MX-300 2022-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 148.74 100 0.069 9.1 4.2 35989 62.87
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 2.7 2.83 0.56
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 2.7 49.58 1.35 35989 1831 98.78 0.234 0.2323 0.2327 0.2652 0.264 96.16
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 10.4604 f_angle_d 0.5112 f_chiral_restr 0.0407 f_plane_restr 0.0031 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3804 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing