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E. coli endonuclease IV complexed with sulfate, catalytic Fe2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 1 microliter protein mixed with 2 microliter precipitant. Protein: 12.5 mg/ml, 20 mM Tris-HCl pH 8.0, 150 mM NaCl.
Precipitant: 0.1 M HEPES pH 7.0, 15% Polyethylene Glycol 3,350, 10 mM Magnesium chloride hexahydrate, 5 mM nickel (II) chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.78 α = 90 b = 115.98 β = 90 c = 177.7 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 PIXEL DECTRIS EIGER X 16M 2023-11-29 M SINGLE WAVELENGTH 2 1 x-ray 170 PIXEL DECTRIS EIGER X 16M 2023-11-29 M SINGLE WAVELENGTH 3 1 x-ray 170 PIXEL DECTRIS EIGER X 16M 2023-11-29 M SINGLE WAVELENGTH 4 1 x-ray 170 PIXEL DECTRIS EIGER X 16M 2023-11-29 M SINGLE WAVELENGTH 5 1 x-ray 170 PIXEL DECTRIS EIGER X 16M 2023-11-29 M SINGLE WAVELENGTH 6 1 x-ray 170 PIXEL DECTRIS EIGER X 16M 2023-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.7712 Diamond I03 2 SYNCHROTRON DIAMOND BEAMLINE I03 1.6984 Diamond I03 3 SYNCHROTRON DIAMOND BEAMLINE I03 1.5028 Diamond I03 4 SYNCHROTRON DIAMOND BEAMLINE I03 1.4760 Diamond I03 5 SYNCHROTRON DIAMOND BEAMLINE I03 1.3051 Diamond I03 6 SYNCHROTRON DIAMOND BEAMLINE I03 1.2782 Diamond I03
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 1.9 97.12 87.8 0.06475 0.07067 0.998 14.86 5.8 193287 22.18
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 1.9 1.92 21.7 0.3256 0.4496 0.3083 0.772 1.36 1.4
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 1QTW 1.9 97.12 1.35 192678 9776 87.75 0.159 0.1565 0.1565 0.2068 0.2068 23.66
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 14.2939 f_angle_d 0.9674 f_chiral_restr 0.0556 f_plane_restr 0.0113 f_bond_d 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10994 Nucleic Acid Atoms Solvent Atoms 1118 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing