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Structure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AY0 PDB entry 2AY0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 30% PEG-MME 550, 50 mM CaCl2, and 100 mM Bis-Tris pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.911 α = 90 b = 44.084 β = 101.5 c = 55.23 γ = 90
Symmetry Space Group C 1 2 1
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 NOIR-1 2006-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.24 ALS 4.2.2
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 2.25 54.153 99.5 0.059 0.059 8.2 3.6 10293
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) 1 2.25 2.37 99.3 0.434 0.434 1.6 3.6 1488
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 2AY0 2.25 54.15 10293 10293 524 99.29 0.208 0.208 0.206 0.2125 0.246 0.2397 RANDOM 44.736
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] -1.48 0.22 0.82 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.617 r_dihedral_angle_4_deg 19.637 r_dihedral_angle_3_deg 15.653 r_dihedral_angle_1_deg 5.638 r_scangle_it 2.056 r_angle_refined_deg 1.591 r_scbond_it 1.404 r_mcangle_it 1.157 r_angle_other_deg 1.089 r_mcbond_it 0.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.617 r_dihedral_angle_4_deg 19.637 r_dihedral_angle_3_deg 15.653 r_dihedral_angle_1_deg 5.638 r_scangle_it 2.056 r_angle_refined_deg 1.591 r_scbond_it 1.404 r_mcangle_it 1.157 r_angle_other_deg 1.089 r_mcbond_it 0.631 r_symmetry_vdw_other 0.237 r_nbtor_refined 0.208 r_nbd_other 0.188 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.181 r_nbd_refined 0.175 r_mcbond_other 0.148 r_nbtor_other 0.078 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_symmetry_hbond_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 709 Nucleic Acid Atoms 757 Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CNS refinement SCALA data scaling PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction CNS phasing