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DNA-binding domain of a p53 homolog from the hydrothermal vent annelid Alvinella pompejana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein solution: 7.2 mg/ml in 25 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM TCEP. Crystallization buffer: 22% PEG 3350, 0.2M MgCl2, 0.1M Tris, pH 8.3. Drop size: 300 nL (150 + 150). Crystals were cryoprotected with mother liquor supplemented with 23% ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.57 52.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.9 α = 88.074 b = 69.985 β = 89.919 c = 114.849 γ = 81.512
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 EIGER X 16M 2020-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999987 SLS X06SA
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 1.92 49.74 92.5 0.056 0.998 12.5 3.7 121535 34.7956466692
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 1.92 1.95 93 0.835 0.63 1.7 3.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2XWR 1.92 46.7 1.95913396015 121501 6025 92.4784789509 0.185582919887 0.18349286792 0.225361909238 0.237 38.2079670174
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 17.212863598 f_angle_d 0.831446041275 f_chiral_restr 0.0561862041547 f_bond_d 0.00703860695921 f_plane_restr 0.0057678334352
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11841 Nucleic Acid Atoms Solvent Atoms 860 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing