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Crystal structure of HpaR-DNA complex from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 100 mM sodium HEPES; MOPS, pH 7.5, 20 mM DL-glutamic acid, 20 mM DL-alanine, 20 mM glycine, 20 mM DL-lysine, 20 mM DL-serine, 20 % (v/v) glycerol and 10 % (v/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.7 54.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.423 α = 81.135 b = 55.15 β = 66.793 c = 57.072 γ = 67.965
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX300HE 2020-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 1.7 27.61 96.9 0.022 0.028 0.017 1 19.1 2.4 52505 19.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.994 5.2
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 7EL2 1.7 27.61 1.99 52376 4914 95.05 0.1657 0.1642 0.164 0.1926 0.1942 32.24
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 26.6757 f_angle_d 1.2364 f_chiral_restr 0.0641 f_plane_restr 0.0099 f_bond_d 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2230 Nucleic Acid Atoms 937 Solvent Atoms 427 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection DIALS data reduction PHASER phasing Aimless data scaling