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E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.29 α = 90 b = 175.44 β = 90.01 c = 84.33 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2015-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
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 1.35 65.29 97.7 0.067 0.073 0.028 0.999 17 6.9 403735 13.6
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 1.35 1.39 94.6 1.623 1.755 0.66 0.429 6.9
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 FOURIER SYNTHESIS THROUGHOUT 5NJ5 1.35 65.29 383738 19995 97.64 0.1468 0.145 0.1533 0.1828 0.1883 RANDOM 16.998
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] -18.18 0.52 13.3 4.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_sphericity_free 18.862 r_dihedral_angle_4_deg 15.524 r_dihedral_angle_3_deg 12.298 r_sphericity_bonded 8.629 r_dihedral_angle_1_deg 5.999 r_rigid_bond_restr 2.49 r_angle_refined_deg 1.38 r_angle_other_deg 0.929 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_sphericity_free 18.862 r_dihedral_angle_4_deg 15.524 r_dihedral_angle_3_deg 12.298 r_sphericity_bonded 8.629 r_dihedral_angle_1_deg 5.999 r_rigid_bond_restr 2.49 r_angle_refined_deg 1.38 r_angle_other_deg 0.929 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13906 Nucleic Acid Atoms Solvent Atoms 2179 Heterogen Atoms 102
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing