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RNase W from Sulfolobus acidocaldarius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RZA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 HEPES pH 7.5, MgCl2, polyacrylic acid (5,100) sodium salt
Crystal Properties Matthews coefficient Solvent content 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.23 α = 90 b = 76.23 β = 90 c = 84.64 γ = 90
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 2017-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9786 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 28.3 99.6 0.9 8 4.5 30609 31.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.11 99.4 0.4 1.1 4.3
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 2.04 28.3 1.34 30609 1531 99.65 0.1927 0.1915 0.1912 0.2138 0.2115 35.28
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 15.0195 f_angle_d 1.2454 f_chiral_restr 0.0865 f_bond_d 0.0135 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3388 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing BUSTER refinement ARP/wARP model building