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Crystal structure of G56S-propeptide:S324A-subtilisin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E1P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.1M Sodium Acetate (pH 4.6), 10%(v/v) Isopropanol, 0.2M Zinc Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.518 α = 90 b = 67.463 β = 90 c = 74.046 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 BRUKER SMART 6500 2006-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.0 SPring-8 BL44XU
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 1.9 50 99.8 0.098 25.3 26131
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 1.9 1.97 100 0.561 3
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 2E1P 1.9 50 24703 1310 99.91 0.1896 0.18851 0.2095 0.206 RANDOM 27.886
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 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.772 r_scangle_it 5.903 r_dihedral_angle_1_deg 5.444 r_scbond_it 4.018 r_mcangle_it 2.475 r_angle_refined_deg 2.216 r_mcbond_it 1.563 r_angle_other_deg 1.023 r_symmetry_vdw_refined 0.428 r_symmetry_hbond_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.772 r_scangle_it 5.903 r_dihedral_angle_1_deg 5.444 r_scbond_it 4.018 r_mcangle_it 2.475 r_angle_refined_deg 2.216 r_mcbond_it 1.563 r_angle_other_deg 1.023 r_symmetry_vdw_refined 0.428 r_symmetry_hbond_refined 0.338 r_metal_ion_refined 0.31 r_nbd_refined 0.263 r_xyhbond_nbd_refined 0.244 r_nbtor_other 0.229 r_symmetry_vdw_other 0.226 r_nbd_other 0.22 r_chiral_restr 0.152 r_bond_refined_d 0.032 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2816 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing