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Crystal structure of S9 peptidase (inactive form) from Deinococcus radiodurans R1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.47 294 50mM sodium acetate, pH 4.5, 200mM sodium chloride, 10mM magnesium chloride, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.702 α = 90 b = 195.092 β = 99.97 c = 107.715 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 CCD MARMOSAIC 225 mm CCD mirrors 2015-04-10 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 2.3 48.77 99.8 0.074 0.084 0.044 0.998 16.6 3.8 132199 29.8
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 2.3 2.34 99.9 0.636 0.742 0.38 0.719 2.2 3.8
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 4HXE 2.3 46.867 1.34 132060 6534 99.74 0.1909 0.1894 0.1903 0.2193 0.2203
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 11.898 f_angle_d 0.578 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18355 Nucleic Acid Atoms Solvent Atoms 1052 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement REFMAC refinement Coot model building RESOLVE model building PHENIX model building PHASER phasing Aimless data scaling XDS data reduction MAR345dtb data collection