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Imidazole-triggered RAS-specific subtilisin SUBT_BACAM complexed with YSAM peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1 M TRIS pH 8.0, 0.2 M NaCl, 20% PEG 6K
Crystal Properties Matthews coefficient Solvent content 2 38.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.64 α = 90 b = 58.64 β = 90 c = 125.17 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 S 6M 2017-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.2 58.64 100 0.103 0.105 0.022 0.997 30.6 22.6 69948
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 100 0.118 0.12 0.025 0.996 22.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1spb 1.2 41.5 66407 3448 99.91 0.1101 0.1093 0.1249 0.1617 RANDOM 7.923
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] -0.06 -0.06 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.814 r_rigid_bond_restr 15.53 r_dihedral_angle_3_deg 11.61 r_dihedral_angle_1_deg 10.735 r_dihedral_angle_4_deg 4.833 r_angle_other_deg 2.759 r_angle_refined_deg 2.176 r_chiral_restr 0.142 r_bond_other_d 0.036 r_bond_refined_d 0.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.814 r_rigid_bond_restr 15.53 r_dihedral_angle_3_deg 11.61 r_dihedral_angle_1_deg 10.735 r_dihedral_angle_4_deg 4.833 r_angle_other_deg 2.759 r_angle_refined_deg 2.176 r_chiral_restr 0.142 r_bond_other_d 0.036 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_gen_planes_other 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1873 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PDB_EXTRACT data extraction REFMAC phasing