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Crystal structure of S9 peptidase (inactive state)from Deinococcus radiodurans R1 in P212121
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 5.31 294 50mM Tris-Cl pH 8.5, 200mM ammonium-citrate, 10mM calcium chloride, 14 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.65 53.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.857 α = 90 b = 130.492 β = 90 c = 194.973 γ = 90
Symmetry Space Group P 21 21 21
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 2015-09-29 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 2.4 48.74 100 0.156 0.165 0.052 0.998 14.9 10 119902 26.6
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 2.4 2.44 100 0.865 0.912 0.288 0.876 3 10
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 2.4 48.74 1.33 119705 5987 99.9 0.1866 0.1849 0.1852 0.2169 0.2147 Random selection 32
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 3.698 f_angle_d 0.877 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 17926 Nucleic Acid Atoms Solvent Atoms 960 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement Coot model building PHASER phasing Aimless data scaling XDS data reduction MAR345dtb data collection