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Isoreticular, interpenetrating co-crystal of protein variant Replication Initiator Protein REPE54 (L53G,Q54G,E55G) and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence.
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 8 298 350 mM MgCl2, 30% PEG 400, and 100 mM Tris HCl
Crystal Properties Matthews coefficient Solvent content 3.27 66.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.11 α = 90 b = 129.426 β = 90 c = 136.826 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 3.15 34.21 98.05 0.127 0.1377 0.05251 0.996 15.68 7 11671 64.14
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 3.15 3.263 99.31 0.5253 0.566 0.2084 0.962 4.99 7.5
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 3.15 34.21 1.33 11512 1147 98.13 0.2479 0.246 0.2458 0.2642 0.2619 85.76
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 27.6303 f_angle_d 0.946 f_chiral_restr 0.0713 f_bond_d 0.0062 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1768 Nucleic Acid Atoms 1273 Solvent Atoms 33 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XSCALE data scaling SCALA data scaling PHASER phasing