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Crystal structure of mature form of Tk-subtilisin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E1P PDB ENTRY 2E1P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 0.1M Sodium Acetate trihydrate, 0.2M Ammonium Sulfate, 25% (w/v) PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.95 37.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.055 α = 90 b = 60.958 β = 90 c = 91.91 γ = 90
Symmetry Space Group P 21 21 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 RIGAKU JUPITER 210 2006-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 1.7 50 99.5 0.054 46.8 29017
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 1.7 1.76 99.1 0.222 7.6
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 2E1P 1.7 32.62 27357 1462 99.8 0.14002 0.13894 0.151 0.16025 0.1736 RANDOM 12.305
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] -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.899 r_dihedral_angle_1_deg 5.008 r_scangle_it 4.278 r_scbond_it 2.756 r_angle_refined_deg 1.676 r_mcangle_it 1.601 r_mcbond_it 0.958 r_angle_other_deg 0.851 r_nbd_refined 0.281 r_symmetry_hbond_refined 0.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.899 r_dihedral_angle_1_deg 5.008 r_scangle_it 4.278 r_scbond_it 2.756 r_angle_refined_deg 1.676 r_mcangle_it 1.601 r_mcbond_it 0.958 r_angle_other_deg 0.851 r_nbd_refined 0.281 r_symmetry_hbond_refined 0.272 r_symmetry_vdw_refined 0.223 r_nbd_other 0.209 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_other 0.171 r_metal_ion_refined 0.112 r_chiral_restr 0.111 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2322 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing