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Crystal structure of a two-domain IdeR-DNA complex crystal form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ISZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 26% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris HCl pH 8.5, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.97 58.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.009 α = 108.95 b = 70.363 β = 103.08 c = 79.569 γ = 94.84
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.1217 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.6 72.481 96.3 0.126 0.126 3.8 1.9 31514
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.74 95.9 0.348 0.348 2 1.9 4585
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2ISZ 2.6 50 31507 1595 96.33 0.229 0.226 0.2266 0.273 0.2721 RANDOM 25.542
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] 0.65 0.09 1.63 -0.16 -0.32 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.173 r_dihedral_angle_4_deg 18.756 r_dihedral_angle_3_deg 16.986 r_dihedral_angle_1_deg 4.723 r_mcangle_it 1.54 r_scangle_it 1.424 r_angle_refined_deg 1.19 r_scbond_it 0.946 r_mcbond_it 0.935 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.173 r_dihedral_angle_4_deg 18.756 r_dihedral_angle_3_deg 16.986 r_dihedral_angle_1_deg 4.723 r_mcangle_it 1.54 r_scangle_it 1.424 r_angle_refined_deg 1.19 r_scbond_it 0.946 r_mcbond_it 0.935 r_nbtor_refined 0.324 r_symmetry_hbond_refined 0.256 r_nbd_refined 0.246 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.199 r_chiral_restr 0.068 r_metal_ion_refined 0.038 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4484 Nucleic Acid Atoms 1347 Solvent Atoms 33 Heterogen Atoms 52
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling