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huCaspase-6 in complex with inhibitor 3a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P4U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M TRIS pH 8.5; 12% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.77 α = 90 b = 60.88 β = 91.41 c = 101.26 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2022-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
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 2.14 49.49 99.9 0.149 0.161 0.062 0.996 10.2 6.8 57282
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 2.14 2.2 100 0.932 1.011 0.388 0.688 6.7
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 3P4U 2.14 49.49 54362 2887 99.88 0.2172 0.2148 0.2194 0.2629 0.2675 RANDOM 31.279
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] -0.9 -0.03 -1.66 2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.517 r_dihedral_angle_4_deg 20.176 r_dihedral_angle_3_deg 13.072 r_dihedral_angle_1_deg 7.13 r_angle_refined_deg 1.337 r_angle_other_deg 1.186 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.517 r_dihedral_angle_4_deg 20.176 r_dihedral_angle_3_deg 13.072 r_dihedral_angle_1_deg 7.13 r_angle_refined_deg 1.337 r_angle_other_deg 1.186 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7819 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 136
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing