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Crystal Structure of Active Human Granzyme M
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DST PDB ENTRY 1DST
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 0.1M BICINE, 0.2M Li2SO4, 0.1M MGCL2, 19% PEG3350, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.46 64.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.391 α = 90 b = 74.391 β = 90 c = 113.199 γ = 120
Symmetry Space Group P 31 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 93 CCD MAR CCD 165 mm 2007-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.000 BSRF 3W1A
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 1.96 50 98.5 0.065 28 6.1 26720 26319 30
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 1.96 2.01 92.1 0.34 2.08 3.6 1596
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 PDB ENTRY 1DST 1.96 32.56 24940 1327 98.66 0.21166 0.20925 0.2058 0.25701 0.254 RANDOM 41.285
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.58 r_dihedral_angle_4_deg 21.308 r_dihedral_angle_3_deg 15.701 r_dihedral_angle_1_deg 6.398 r_scangle_it 3.866 r_scbond_it 2.534 r_angle_refined_deg 1.726 r_mcangle_it 1.632 r_mcbond_it 1.083 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.58 r_dihedral_angle_4_deg 21.308 r_dihedral_angle_3_deg 15.701 r_dihedral_angle_1_deg 6.398 r_scangle_it 3.866 r_scbond_it 2.534 r_angle_refined_deg 1.726 r_mcangle_it 1.632 r_mcbond_it 1.083 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.121 r_symmetry_hbond_refined 0.111 r_bond_refined_d 0.023 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1748 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing