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Crystal structure of SarF, the ComR paralog from S.salivarius, in complex with DNA and the synthetic peptide sBI7.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 290 30% PEG 4000, 0.2M ammonium sulfate, 0.1M NA acetate
Crystal Properties Matthews coefficient Solvent content 3.17 61.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.43 α = 90 b = 112.02 β = 106.14 c = 160.85 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 9M 2019-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.49 47.22 99.4 0.068 0.086 0.999 6.48 6.96 39614 142.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.49 3.7 1.146 1.453 0.374
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.49 47.22 39614 1981 99.4 0.283 0.2812 0.2834 0.3159 0.3063 RANDOM 172.86
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] 8.4349 -6.124 5.4108 -13.8457
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.75 t_omega_torsion 2.09 t_angle_deg 0.73 t_bond_d 0.005 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.75 t_omega_torsion 2.09 t_angle_deg 0.73 t_bond_d 0.005 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15202 Nucleic Acid Atoms 2202 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing