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Crystal structure of LARP1-unique domain DM15 bound to m7GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES, pH 7.5 and 10% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.2 43.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.177 α = 90 b = 60.163 β = 101.28 c = 60.609 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS HTC 2016-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.77 33.895 86 2.45 2.9 28525
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4ZC4 1.77 33.895 27251 1923 81.92 0.1787 0.1763 0.1811 0.2094 0.2107
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 13.357 f_angle_d 0.481 f_chiral_restr 0.029 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2626 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement Coot model building HKL-2000 data scaling PHENIX phasing