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Structure of Thermolysin in complex with N-Carbobenzyloxy-L-aspartic acid and L-Phenylalanine Methyl Ester
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TLN PDB entry 8TLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 THERMOLYSIN WAS DISSOLVED IN 30% DMSO, 36mM TRIS/HCl, 1M CALCIUM ACETATE pH 6.3 AT 100MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 47.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.686 α = 90 b = 92.686 β = 90 c = 128.764 γ = 120
Symmetry Space Group P 61 2 2
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 monochromatic vertical focusing 2010-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.9202 CHESS F2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 100 99.7 0.058 0.092 22.9 13.4 52878 52719
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.539 98.1 0.907 0.899 2.1 10.3 5082
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 8TLN 1.5 27.44 52816 49604 2652 98.94 0.14576 0.14576 0.1436 0.1459 0.18707 0.188 RANDOM 15.555
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] -0.05 -0.02 -0.05 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.559 r_dihedral_angle_4_deg 16.229 r_dihedral_angle_3_deg 11.784 r_dihedral_angle_1_deg 5.642 r_scangle_it 4.841 r_scbond_it 3.364 r_mcangle_it 2.117 r_angle_refined_deg 1.468 r_mcbond_it 1.379 r_rigid_bond_restr 1.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.559 r_dihedral_angle_4_deg 16.229 r_dihedral_angle_3_deg 11.784 r_dihedral_angle_1_deg 5.642 r_scangle_it 4.841 r_scbond_it 3.364 r_mcangle_it 2.117 r_angle_refined_deg 1.468 r_mcbond_it 1.379 r_rigid_bond_restr 1.248 r_angle_other_deg 0.95 r_mcbond_other 0.446 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2432 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 84
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling