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Room temperature structure of RNase A at 100 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 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.4 α = 90 b = 64.4 β = 90 c = 64.75 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 1.55 28 98.73 0.1619 0.064 0.988 6.11 6.8 22676 21.53
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 1.55 1.61 99.6 1.905 0.7833 0.306 1.01 6.6
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 1.55 28 1.34 22673 1780 98.75 0.1582 0.1558 0.158 0.1878 0.1884 34.88
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 11.9049 f_angle_d 1.0445 f_chiral_restr 0.0545 f_bond_d 0.0096 f_plane_restr 0.0069
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 Coot model building XDS data reduction XSCALE data scaling PHASER phasing