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Rhodococcus hoagii DnaA DI in the P6(2)22 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other different model solved in this study
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% (w/v) PEG 1000, 100 mM Sodium acetate/acetic acid pH 4.5, 200 mM Zinc acetate
Crystal Properties Matthews coefficient Solvent content 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.1 α = 90 b = 61.1 β = 90 c = 132.81 γ = 120
Symmetry Space Group P 62 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 PIXEL RIGAKU HyPix-6000HE 2024-02-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 20.69 99.7 0.132 0.033 0.999 16.2 15.9 3312 64.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 100 0.483 0.114 0.993 4 17.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3 20.42 1.34 3245 162 98.66 0.2201 0.218 0.2183 0.2607 0.2569 61.5
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 5.2601 f_angle_d 0.693 f_chiral_restr 0.0422 f_plane_restr 0.0051 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 673 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling PHASER phasing