☰ Navigation Tabs
Crystal structure of P. furiosus SRP54 NG domain T116del
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Protein concentrated to 9.8 mg/mL in SEC buffer: 20mM Tris-HCl pH 8.0, 100mM NaCl
Crystallization buffer: 220mM ammonium citrate, pH 5.1, 20% PEG 3,350
Crystallized by mixing protein solution with crystallization buffer in a 1:1 v/v ratio
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.123 α = 90 b = 66.236 β = 90 c = 104.265 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS EIGER2 X CdTe 16M 2022-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033201 APS 23-ID-D
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 1.444 41.41 98.92 0.0906 0.09465 0.027 0.999 13.71 12.1 56783 5.91
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 1.444 1.496 89.47 1.992 2.105 0.6619 0.554 9.8
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 1.44 41.41 1.33 106990 3755 97.02 0.2141 0.213 0.2027 0.2445 0.2356 29.14
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 16.8249 f_angle_d 0.9876 f_chiral_restr 0.0844 f_bond_d 0.0097 f_plane_restr 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2245 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing