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Crystal structure of pyrrolidone carboxylate peptidase I with disordered loop A from Deinococcus radiodurans R1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 294 0.2M NaCl, 0.1M Bis-tris pH 6.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.317 α = 90 b = 47.171 β = 105.66 c = 105.537 γ = 90
Symmetry Space Group I 1 2 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 2017-09-28 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 1.7 38.33 99.3 0.06 0.07 0.037 0.998 13.7 3.7 46549 15.5
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 1.7 1.73 99.9 0.498 0.586 0.388 0.875 2.7 3.7
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 5Z40 1.7 29.77 1.34 46547 2251 99.34 0.2083 0.2067 0.2064 0.2394 0.237
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 14.604 f_angle_d 0.871 f_chiral_restr 0.056 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3082 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing Aimless data scaling XDS data reduction MAR345dtb data collection