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The Oligomeric Structure of Human Granzyme A Reveals the Molecular Determinants of Substrate Specificity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DST
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Tris pH 8.5, PEG 4000, lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.14 60.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.034 α = 90 b = 145.022 β = 90 c = 39.555 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 4 2002-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.4 20 99.5 13319 12664
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 94.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DST 2.4 20 13319 12664 660 99.46 0.19339 0.19137 0.19137 0.23245 RANDOM 35.985
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] -1.98 2.91 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.345 r_scangle_it 3.433 r_scbond_it 2.039 r_angle_refined_deg 1.543 r_mcangle_it 1.39 r_mcbond_it 0.713 r_symmetry_vdw_refined 0.4 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.345 r_scangle_it 3.433 r_scbond_it 2.039 r_angle_refined_deg 1.543 r_mcangle_it 1.39 r_mcbond_it 0.713 r_symmetry_vdw_refined 0.4 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1774 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing