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Crystal structure of peptidase E with ordered active site loop from Salmonella enterica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 294 0.1 M Bis-tris pH6.5, 0.2 M Sodium Chloride, 25 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.17 43.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.452 α = 90 b = 42.933 β = 106.39 c = 89.149 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97949 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 45.77 99.4 0.053 0.064 0.035 0.998 16.9 3.2 38789 20.7
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 99.3 0.388 0.465 0.254 0.886 3.2 3.1
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 1FY2 1.9 41.461 1.34 38756 1887 99.18 0.1834 0.182 0.1835 0.211 0.2132 23
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 13.779 f_angle_d 0.874 f_chiral_restr 0.056 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3530 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing Aimless data scaling XDS data reduction MAR345dtb data collection