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Structure of the DNA-binding domain of E. Coli Proline Utilization A (PUTA)
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 6.5 295 0.05M AMMONIUM SULFATE, 0.05M
BIS-TRIS, 30% PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH). N-TERMINAL
HIS TAG REMOVED BY TREATMENT WITH TEV PROTEASE , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.08 40.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.731 α = 90 b = 55.731 β = 90 c = 125.019 γ = 90
Symmetry Space Group P 41 21 2
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 2006-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.2398 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 1.9 50.9 100 0.043 25.5 13.03 16253 2 32.313
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 1.9 1.97 98 0.317 5.7 8.29
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 (All) 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 1.9 50.9 16185 815 99.61 0.205 0.203 0.203 0.249 0.2474 RANDOM 35.941
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] 0.98 0.98 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.136 r_dihedral_angle_4_deg 18.31 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_1_deg 3.325 r_scangle_it 1.641 r_angle_refined_deg 1.09 r_scbond_it 1.069 r_mcangle_it 0.562 r_mcbond_it 0.392 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.136 r_dihedral_angle_4_deg 18.31 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_1_deg 3.325 r_scangle_it 1.641 r_angle_refined_deg 1.09 r_scbond_it 1.069 r_mcangle_it 0.562 r_mcbond_it 0.392 r_nbtor_refined 0.293 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.156 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1470 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 20
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction