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Complex of subtilase SubTY from Bacillus sp. TY145 with chymotrypsin inhibitor CI2A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 Complex was concentrated to 45 mg/ml in 10 mM Tris, pH 7.0. 1 microliter of protein solution with 1 microliter of a reservoir solution containing 5.5 M sodium formate, 0.2 M imidazole-malate pH 6.5, and 200 mM NDSB 201.
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.753 α = 90 b = 66.838 β = 90 c = 107.082 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 120 IMAGE PLATE MAR scanner 345 mm plate 2001-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54178
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 1.8 25 100 0.07 33 8.4 40054 40054 -3 17.676
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 1.8 1.83 99.6 0.347 5.8
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 1SVN 1.8 25 38044 2009 99.88 0.15285 0.15098 0.1621 0.18839 0.1947 RANDOM 14.614
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] 0.28 -0.81 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_4_deg 16.02 r_dihedral_angle_3_deg 13.185 r_dihedral_angle_1_deg 6.161 r_scangle_it 3.61 r_scbond_it 2.361 r_angle_refined_deg 1.509 r_mcangle_it 1.463 r_angle_other_deg 0.88 r_mcbond_it 0.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.192 r_dihedral_angle_4_deg 16.02 r_dihedral_angle_3_deg 13.185 r_dihedral_angle_1_deg 6.161 r_scangle_it 3.61 r_scbond_it 2.361 r_angle_refined_deg 1.509 r_mcangle_it 1.463 r_angle_other_deg 0.88 r_mcbond_it 0.877 r_mcbond_other 0.28 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.211 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.172 r_symmetry_vdw_other 0.165 r_metal_ion_refined 0.099 r_chiral_restr 0.095 r_symmetry_vdw_refined 0.094 r_nbtor_other 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2753 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing XTALVIEW model building