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Room temperature structure of RNase A at 50 MPa helium gas pressure in a sapphire capillary
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 295 10-20 mg/ml protein dissolved in 0.1 M sodium acetate pH 4.5 was mixed in a 1:1 ratio with precipitant containing 0.1 M sodium acetate pH 4.5, 1.2-1.5 M ammonium sulphate and 2-2.5 M sodium chloride and equilibrated for one to two days at room-temperature.
Crystal Properties Matthews coefficient Solvent content 2.84 56.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.49 α = 90 b = 64.49 β = 90 c = 64.93 γ = 120
Symmetry Space Group P 32 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 295 PIXEL DECTRIS PILATUS3 X CdTe 2M 2019-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.477 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 27.92 98.76 0.1792 0.072 0.987 5.83 6.8 20806 22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.657 99.23 2.115 0.8893 0.334 1.08
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2E3W 1.6 27.92 1.34 20788 1633 98.8 0.1563 0.1538 0.1554 0.1876 0.1898 34.38
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 12.3491 f_angle_d 1.0446 f_chiral_restr 0.0524 f_bond_d 0.0088 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 951 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing