☰ Navigation Tabs
Structure of the E. coli PutA proline dehydrogenase domain reduced by dithionite and complexed with SO2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TJ0 PDB Entry: 1TJ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 293 Crystals were grown in 13-15% PEG 3350, 60-190 mM citrate buffer. Prior to data collection a crystal was soaked in excess Na dithionite in order to reduce the FAD cofactor., pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.82 56.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.11 α = 90 b = 141.424 β = 90 c = 145.7 γ = 90
Symmetry Space Group I 2 2 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 ADSC QUANTUM 4 2003-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97856 APS 19-ID
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 2.3 50 98.2 0.071 9.7 33078
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 2.3 2.38 94.2 0.465
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-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: 1TJ0 2.3 46.13 33071 1635 100 0.212 0.212 0.209 0.2142 0.257 0.2605 RANDOM 36.941
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] -0.6 4.69 -4.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.447 r_scangle_it 3.444 r_scbond_it 2.126 r_angle_refined_deg 1.446 r_mcangle_it 1.364 r_angle_other_deg 0.829 r_mcbond_it 0.726 r_nbd_other 0.229 r_symmetry_vdw_other 0.22 r_nbd_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.447 r_scangle_it 3.444 r_scbond_it 2.126 r_angle_refined_deg 1.446 r_mcangle_it 1.364 r_angle_other_deg 0.829 r_mcbond_it 0.726 r_nbd_other 0.229 r_symmetry_vdw_other 0.22 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.14 r_nbtor_other 0.086 r_chiral_restr 0.076 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3460 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction