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Structure of the Lys9Met mutant of the E. coli Proline Utilization A (PutA) DNA-binding domain.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 1.7-3.0 M NaCl, 5 mM dithiothreitol, pH 3.0-5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.07 α = 90 b = 91.494 β = 119.21 c = 69.606 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 173 CCD CUSTOM-MADE 2004-12-08 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.987121, 0.979553, 0.979144 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 60.75 100 0.079 12.5 7.47 26606 26606
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 0.52 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 2.1 60.75 26606 21873 1153 99.88 0.20597 0.204 0.2125 0.2418 0.2461 RANDOM 38.245
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] 0.61 -0.67 0.11 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.346 r_dihedral_angle_3_deg 15.652 r_dihedral_angle_4_deg 14.232 r_dihedral_angle_1_deg 4.667 r_scangle_it 2.473 r_scbond_it 1.637 r_angle_refined_deg 1.139 r_mcangle_it 1.007 r_angle_other_deg 0.774 r_mcbond_it 0.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.346 r_dihedral_angle_3_deg 15.652 r_dihedral_angle_4_deg 14.232 r_dihedral_angle_1_deg 4.667 r_scangle_it 2.473 r_scbond_it 1.637 r_angle_refined_deg 1.139 r_mcangle_it 1.007 r_angle_other_deg 0.774 r_mcbond_it 0.732 r_symmetry_vdw_refined 0.253 r_nbd_refined 0.219 r_nbtor_refined 0.171 r_nbd_other 0.167 r_symmetry_vdw_other 0.167 r_xyhbond_nbd_refined 0.147 r_mcbond_other 0.137 r_symmetry_hbond_refined 0.097 r_nbtor_other 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2072 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 6
Software Software Software Name Purpose d*TREK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection