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Crystal structure of human granzyme H with a peptidyl substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TK9 PDB ENTRY 3TK9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 0.2M Li2SO4, 0.1M Bicine (pH 8.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.28 46.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.848 α = 90 b = 57.848 β = 90 c = 142.771 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 CCD ADSC QUANTUM 315r 2010-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50 98.8 0.08 30.16 29.4 10114 9993 -0.5 38.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 92.9 0.317 3.4 12.3 907
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3TK9 2.4 50 9993 9482 478 99.07 0.248 0.23403 0.23357 0.2232 0.24286 0.2314 RANDOM 20.151
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] 1.05 1.05 -2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.444 r_dihedral_angle_4_deg 15.228 r_dihedral_angle_3_deg 14.191 r_dihedral_angle_1_deg 4.109 r_scangle_it 3.387 r_scbond_it 2.038 r_mcangle_it 1.547 r_angle_refined_deg 1.25 r_mcbond_it 0.836 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.444 r_dihedral_angle_4_deg 15.228 r_dihedral_angle_3_deg 14.191 r_dihedral_angle_1_deg 4.109 r_scangle_it 3.387 r_scbond_it 2.038 r_mcangle_it 1.547 r_angle_refined_deg 1.25 r_mcbond_it 0.836 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1823 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 10
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing