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Replication Initiator Protein REPE54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (5 mg/mL EDC, 12 hours).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 90 mM MgCl2, 3% PEG 400, and 220 mM Tris HCl.
Crystal Properties Matthews coefficient Solvent content 3.22 61.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.993 α = 90 b = 79.181 β = 123.023 c = 74.903 γ = 90
Symmetry Space Group C 1 2 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 CMOS RDI CMOS_8M 2021-04-16 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 3.14 37.05 97.3 0.085 0.1 0.052 0.997 6.6 3.6 9433 83.36
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 3.14 3.36 96.2 0.408 0.48 0.251 0.965 1.8 3.6
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 7rva 3.14 37.05 1.36 9289 498 95.89 0.1972 0.1934 0.1937 0.2632 0.2642 109.8
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 25.7445 f_angle_d 1.4797 f_chiral_restr 0.0795 f_bond_d 0.0124 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1818 Nucleic Acid Atoms 863 Solvent Atoms 3 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XSCALE data scaling SCALA data scaling PHASER phasing