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Crystal structure of P. furiosus SRP54 NG domain wild type
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Crystal structure of P. furiosus SRP54 NG T115del, crystallized and analyzed in our own group.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Purification: 13.3 mg/mL, in 20 mM Tris-HCl pH 8.0, 100 mM NaCl
Crystallization condition: 100mM sodium phosphate dibasic/ citric acid pH 4.2, 200mM NaCl, 20% w/v PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.042 α = 90 b = 45.04 β = 113.96 c = 96.407 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 PIXEL DECTRIS EIGER X 9M 2024-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920119 NSLS-II 17-ID-1
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 1.83 33.98 98.8 0.1331 0.1623 0.09165 0.987 5.49 3.01 54546 26.21
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 1.83 1.895 99.58 1.018 1.239 0.6973 0.443 1.02 3.04
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 1.83 33.98 1.34 54546 2000 98.83 0.1962 0.195 0.1957 0.2264 0.2233 28.85
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 8.5687 f_angle_d 0.8687 f_chiral_restr 0.0578 f_bond_d 0.008 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4562 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 40
Software Software Software Name Purpose XDS data reduction PHENIX refinement PHENIX phasing Coot model building Aimless data scaling