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RNase A-Adenosine 5'-Heptaphosphate (RNaseA.p7A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AFU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 25% PEG4000, 20 mM citrate, pH 6, crystal soaked in 50 mM ligand, 30% PEG4000, 25% glycerol, 20 mM citrate
Crystal Properties Matthews coefficient Solvent content 1.96 37.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.383 α = 90 b = 31.347 β = 90.67 c = 68.962 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 CCD APEX II CCD 2023-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.544178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.68 34.48 99.9 0.0292 3.55 10.43 24657 22.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.78 0.396
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 PDB entry 1AFU 1.68 34.48 1.33 24468 1195 99.21 0.2124 0.211 0.2111 0.2367 0.2368 27.96
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 6.6846 f_angle_d 1.0258 f_chiral_restr 0.0577 f_plane_restr 0.0083 f_bond_d 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1894 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 94
Software Software Software Name Purpose PHENIX refinement PHENIX refinement SAINT data reduction SADABS data scaling PHENIX phasing