☰ Navigation Tabs
Crystal structure of S9 peptidase (S514A mutant in inactive state) from Deinococcus radiodurans R1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.28 294 40mM potassium phosphate, 16% PEG 8000, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.92 57.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.415 α = 90 b = 189.2 β = 108.59 c = 121.03 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 2018-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 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 2.6 47.3 99.7 0.096 0.113 0.059 0.995 11.4 3.5 100840 38.3
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 2.6 2.64 99.9 0.71 0.845 0.454 0.743 2.1 3.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5YZM 2.6 39.756 1.34 100744 4982 99.61 0.2181 0.2163 0.219 0.2527 0.2534 random selection
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 3.492 f_angle_d 0.711 f_chiral_restr 0.053 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18284 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing Aimless data scaling XDS data reduction MAR345dtb data collection