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Crystal structure of M1 zinc metallopeptidase E323A mutant bound to Tyr-ser-ala substrate from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.5 294 0.2M Ammonium formate, 0.1M Bis-tris pH 5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.84 33.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.598 α = 89.77 b = 57.594 β = 82.14 c = 69.321 γ = 67.8
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 2018-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.979470 RRCAT INDUS-2 PX-BL21
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 1.9 44.83 97.7 0.052 0.065 0.039 0.997 14.2 2.7 56301 13.046
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 1.9 1.94 96.3 0.352 0.446 0.269 0.865 3.2 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6A8Z 1.9 24.137 1.98 56240 2750 97.6 0.1821 0.1805 0.1809 0.2142 0.2136
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.043 f_angle_d 0.796 f_chiral_restr 0.05 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6658 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing Aimless data scaling XDS data reduction MAR345dtb data collection