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Thermolysin Room-Temperature In-Situ, Grown On-Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.20 M sodium di-hydrogen phosphate,
16.7% polyethylene glycol (PEG) 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.073 α = 90 b = 93.073 β = 90 c = 130.561 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 293 PIXEL DECTRIS EIGER2 X 4M 2024-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.7749 Diamond VMXi
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.73 80.6 100 0.181 0.197 0.077 0.998 9.8 11.5 35537
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.73 1.76 100 1.95 2.352 1.292 0.288 0.8 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.73 80.6 35485 1844 99.972 0.148 0.1469 0.1452 0.1726 0.1713 20.431
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] -0.144 -0.072 -0.144 0.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.891 r_lrange_it 13.043 r_dihedral_angle_3_deg 12.157 r_lrange_other 11.738 r_dihedral_angle_2_deg 7.471 r_dihedral_angle_1_deg 5.887 r_scangle_it 4.458 r_scangle_other 4.457 r_scbond_it 2.925 r_scbond_other 2.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.891 r_lrange_it 13.043 r_dihedral_angle_3_deg 12.157 r_lrange_other 11.738 r_dihedral_angle_2_deg 7.471 r_dihedral_angle_1_deg 5.887 r_scangle_it 4.458 r_scangle_other 4.457 r_scbond_it 2.925 r_scbond_other 2.919 r_mcangle_it 2.164 r_mcangle_other 2.164 r_angle_refined_deg 1.757 r_mcbond_it 1.558 r_mcbond_other 1.55 r_angle_other_deg 0.627 r_symmetry_xyhbond_nbd_refined 0.442 r_symmetry_nbd_refined 0.271 r_nbd_refined 0.234 r_nbd_other 0.205 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.148 r_metal_ion_refined 0.115 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2412 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling Coot model building xia2.multiplex data reduction MOLREP phasing