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Thermolysin Room-Temperature In-Situ, Shipped
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 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.032 α = 90 b = 93.032 β = 90 c = 130.452 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 2024-09-25 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 1.66 80.57 98.8 0.132 0.143 0.054 0.998 11.2 10.9 39612
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) 1.66 1.69 91 1.611 1.934 1.024 0.368 0.5 4.6
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 1.66 80.568 39545 1991 98.865 0.162 0.1605 0.1604 0.1831 0.1831 21.317
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] -0.164 -0.082 -0.164 0.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.05 r_dihedral_angle_3_deg 13.061 r_lrange_it 10.977 r_dihedral_angle_2_deg 6.508 r_dihedral_angle_1_deg 6.171 r_scangle_it 5.03 r_scbond_it 3.218 r_mcangle_it 2.324 r_angle_refined_deg 1.78 r_mcbond_it 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.05 r_dihedral_angle_3_deg 13.061 r_lrange_it 10.977 r_dihedral_angle_2_deg 6.508 r_dihedral_angle_1_deg 6.171 r_scangle_it 5.03 r_scbond_it 3.218 r_mcangle_it 2.324 r_angle_refined_deg 1.78 r_mcbond_it 1.71 r_symmetry_nbd_refined 0.331 r_nbtor_refined 0.323 r_symmetry_xyhbond_nbd_refined 0.272 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.095 r_metal_ion_refined 0.089 r_gen_planes_refined 0.012 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2420 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement Aimless data scaling Coot model building xia2.multiplex data reduction MOLREP phasing