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X-ray structure of SS-RNase-2 des116-120
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 25% w/v PEG 3350, 0.2 M sodium chloride and 0.1 M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.83 56.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.07 α = 90 b = 93.07 β = 117.19 c = 66.78 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 RIGAKU SATURN 944 2020-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.88 70 96.2 0.889 3.4 3.4 13043
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 2.88 3.06 0.411 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7BFK 2.88 67.46 12745 705 98.92 0.2613 0.2588 0.264 0.3076 0.3106 RANDOM 49.462
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] -0.09 0.09 0.11 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.953 r_dihedral_angle_4_deg 15.171 r_dihedral_angle_3_deg 14.238 r_dihedral_angle_1_deg 5.683 r_angle_refined_deg 1.143 r_angle_other_deg 1.079 r_chiral_restr 0.029 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_refined 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.953 r_dihedral_angle_4_deg 15.171 r_dihedral_angle_3_deg 14.238 r_dihedral_angle_1_deg 5.683 r_angle_refined_deg 1.143 r_angle_other_deg 1.079 r_chiral_restr 0.029 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3334 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing