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Co-crystal structure of Prx with ComR DNA binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CKA PDB entry 6CKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 15 mg/mL protein, 20% PEG3500, 0.2 M potassium acetate
Crystal Properties Matthews coefficient Solvent content 1.53 19.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.556 α = 90 b = 41.918 β = 90 c = 90 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 PIXEL DECTRIS PILATUS3 6M 2020-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.28329 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 45 99.9 0.067 0.027 0.998 15.2 6.1 18234 24.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 100 0.727 0.316 0.867 2.3 6.1
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 PDB entry 6CKA 1.65 45 1.33 18234 1819 99.59 0.1763 0.175 0.1837 0.1971 0.2061 31.74
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 4.9092 f_angle_d 0.6552 f_chiral_restr 0.0461 f_plane_restr 0.0079 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1051 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building PHENIX phasing XDS data reduction XDS data scaling Aimless data scaling