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Structural insights into the proteolytic machinery of apoptosis-inducing Granzyme M
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GZC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 20% PEG3350, 0.2M Li2SO4, 0.1M Bicine, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.44 64.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.671 α = 90 b = 74.671 β = 90 c = 113.557 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 FLAT PANEL MARRESEARCH Flat Panel 2008-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 1W2B 0.9789 BSRF 1W2B
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 2.7 64.68 95.04 0.094 7.3 10499 9978
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 2GZC 2.7 56.19 9978 501 99.83 0.22609 0.22279 0.2168 0.29308 0.2784 RANDOM 30.385
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] -0.17 -0.09 -0.17 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.365 r_dihedral_angle_4_deg 21.018 r_dihedral_angle_3_deg 17.656 r_dihedral_angle_1_deg 7.377 r_scangle_it 3.219 r_scbond_it 2.018 r_angle_refined_deg 1.88 r_mcangle_it 1.348 r_mcbond_it 0.775 r_symmetry_vdw_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.365 r_dihedral_angle_4_deg 21.018 r_dihedral_angle_3_deg 17.656 r_dihedral_angle_1_deg 7.377 r_scangle_it 3.219 r_scbond_it 2.018 r_angle_refined_deg 1.88 r_mcangle_it 1.348 r_mcbond_it 0.775 r_symmetry_vdw_refined 0.328 r_nbtor_refined 0.32 r_symmetry_hbond_refined 0.275 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1783 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling PHASES phasing