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Crystal structure of the cysteine-free anti-UTag intrabody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7URL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 2M Ammonium Sulfate, 0.1M BIS-TRIS pH7, 3% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.679 α = 90 b = 74.521 β = 90 c = 157.394 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 100 CMOS RDI CMOS_8M 2022-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
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 1.45 42.9 98.05 0.03664 0.05182 0.03664 0.999 11.24 2 84215 16.57
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 1.45 1.49 78.06 0.8496 1.201 0.8496 0.394 1.9
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 1.45 42.9 1.34 84183 2000 98.05 0.1747 0.1737 0.1739 0.2141 0.2131 25.59
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 13.9982 f_angle_d 0.8813 f_chiral_restr 0.0931 f_plane_restr 0.0058 f_bond_d 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3861 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XSCALE data scaling SCALA data scaling PHASER phasing