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Mirolysin in complex with compound 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R7W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M Zinc acetate dihydrate, 0.1 M Sodium acetate pH 4.5, 10% (v/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.593 α = 92.462 b = 77.64 β = 90 c = 81.995 γ = 119.98
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2021-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 2.1 40.95 92.2 0.097 0.137 0.097 0.983 7.8 2.6 88998
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 2.1 2.14 0.24 0.339 0.24 0.93 2.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6r7w 2.1 38.803 88998 4127 92.155 0.205 0.2038 0.2037 0.2304 0.2301 15.477
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] -1.772 -0.437 -0.287 -1.891 0.341 5.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_4_deg 15.971 r_dihedral_angle_3_deg 13.748 r_dihedral_angle_other_3_deg 8.99 r_dihedral_angle_1_deg 7.072 r_lrange_it 5.296 r_lrange_other 5.189 r_scangle_it 2.562 r_scangle_other 2.561 r_mcangle_it 2.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_4_deg 15.971 r_dihedral_angle_3_deg 13.748 r_dihedral_angle_other_3_deg 8.99 r_dihedral_angle_1_deg 7.072 r_lrange_it 5.296 r_lrange_other 5.189 r_scangle_it 2.562 r_scangle_other 2.561 r_mcangle_it 2.356 r_mcangle_other 2.356 r_scbond_it 1.539 r_scbond_other 1.538 r_angle_refined_deg 1.455 r_mcbond_it 1.372 r_mcbond_other 1.369 r_angle_other_deg 1.312 r_symmetry_nbd_refined 0.399 r_symmetry_xyhbond_nbd_refined 0.324 r_xyhbond_nbd_other 0.301 r_nbd_other 0.248 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_other 0.137 r_metal_ion_refined 0.122 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.068 r_ncsr_local_group_3 0.066 r_ncsr_local_group_7 0.064 r_ncsr_local_group_2 0.062 r_ncsr_local_group_5 0.061 r_ncsr_local_group_11 0.061 r_ncsr_local_group_13 0.061 r_ncsr_local_group_4 0.059 r_ncsr_local_group_8 0.059 r_ncsr_local_group_6 0.058 r_ncsr_local_group_9 0.058 r_ncsr_local_group_10 0.058 r_ncsr_local_group_15 0.058 r_ncsr_local_group_14 0.056 r_ncsr_local_group_1 0.054 r_ncsr_local_group_12 0.048 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12659 Nucleic Acid Atoms Solvent Atoms 1067 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing