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Ton1285, an Intracellular Protease from Thermococcus onnurineus NA1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G2I PDB ENTRY 1G2I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8 295 20% PEG 8000, 0.1M HEPES pH7.5, 0.2M Ammonium sulfate, pH 8.0, EVAPORATION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.32 47.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.114 α = 90 b = 87.114 β = 90 c = 80.119 γ = 120
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 210 2009-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0000 PAL/PLS 4A
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 1.78 50 5.9 31234 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.78 50 99.5 4.23 16.1 32912
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1G2I 1.78 29.49 31234 1669 99.9 0.1628 0.16006 0.21451 0.2024 RANDOM 19.725
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.795 r_dihedral_angle_4_deg 17.076 r_dihedral_angle_3_deg 13.172 r_dihedral_angle_1_deg 5.359 r_sphericity_free 4.608 r_scangle_it 3.012 r_sphericity_bonded 2.093 r_scbond_it 2.017 r_angle_refined_deg 1.312 r_rigid_bond_restr 1.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.795 r_dihedral_angle_4_deg 17.076 r_dihedral_angle_3_deg 13.172 r_dihedral_angle_1_deg 5.359 r_sphericity_free 4.608 r_scangle_it 3.012 r_sphericity_bonded 2.093 r_scbond_it 2.017 r_angle_refined_deg 1.312 r_rigid_bond_restr 1.291 r_mcangle_it 1.265 r_mcbond_it 0.892 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.21 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.147 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.094 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_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2653 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing