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Crystal structure of complex between SA-subtilisin and Tk-propeptide with deletion of the two C-terminal residues
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Sodium Cacodylate, 0.2M Zinc Acetate, 2%(w/v) PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.732 α = 90 b = 68.468 β = 90 c = 73.704 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 2008-04-17 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 2.2 50 96.3 0.125 18.3 17483
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 2.2 2.28 80.7 0.384 2.5
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 2Z30 2.2 36.86 15948 843 96.26 0.1727 0.16974 0.17 0.23074 0.2301 RANDOM 29.458
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] 0.06 -0.04 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.049 r_dihedral_angle_4_deg 18.665 r_dihedral_angle_3_deg 17.183 r_dihedral_angle_1_deg 6.992 r_scangle_it 4.11 r_scbond_it 2.843 r_angle_refined_deg 1.843 r_mcangle_it 1.706 r_mcbond_it 1.208 r_symmetry_vdw_refined 0.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.049 r_dihedral_angle_4_deg 18.665 r_dihedral_angle_3_deg 17.183 r_dihedral_angle_1_deg 6.992 r_scangle_it 4.11 r_scbond_it 2.843 r_angle_refined_deg 1.843 r_mcangle_it 1.706 r_mcbond_it 1.208 r_symmetry_vdw_refined 0.339 r_metal_ion_refined 0.331 r_nbtor_refined 0.308 r_xyhbond_nbd_refined 0.249 r_symmetry_metal_ion_refined 0.247 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.19 r_chiral_restr 0.114 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2805 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing