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Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence co-crystallized with a guest small molecule, netropsin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7U6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 300 mM MgCl2, 25% PEG 400, and 100 mM Tris HCl
Crystal Properties Matthews coefficient Solvent content 3.27 66.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.15 α = 90 b = 132.731 β = 90 c = 134.261 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2021-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
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 3.12 38.32 99.24 0.134 0.1449 0.05436 0.998 11.38 7.1 12130 74.24
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 3.12 3.232 99.17 1.18 1.269 0.4648 0.898 1.84 7.4
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 7u6k 3.12 38.32 1.34 12075 1201 99.32 0.1974 0.1933 0.195 0.2336 0.234 94.34
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 27.241 f_angle_d 1.5718 f_chiral_restr 0.0865 f_bond_d 0.0142 f_plane_restr 0.0115
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1764 Nucleic Acid Atoms 1273 Solvent Atoms 17 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XSCALE data scaling SCALA data scaling PHASER phasing