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Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) co-crystallized with L-lactate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K87 PDB ENTRY 1K87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 295 13-15%, PEG 3350, 60-190mM citrate buffer, 10mM L-lactate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.244 α = 90 b = 139.431 β = 90 c = 146.051 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 CUSTOM-MADE APS 19ID 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) 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 2.1 99 99 0.072 0.072 24 6.8 42869 42869 40
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 2.1 2.18 92 0.485 0.485 2.8 5.4 3961
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 1K87 2.1 25.24 43417 40761 2107 99 0.214 0.21412 0.21191 0.217 0.25855 0.2621 RANDOM 26.632
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] -0.68 3.9 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.79 r_scangle_it 3.478 r_scbond_it 2.142 r_angle_refined_deg 1.446 r_mcangle_it 1.38 r_angle_other_deg 0.847 r_mcbond_it 0.748 r_symmetry_vdw_refined 0.288 r_symmetry_vdw_other 0.27 r_nbd_other 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.79 r_scangle_it 3.478 r_scbond_it 2.142 r_angle_refined_deg 1.446 r_mcangle_it 1.38 r_angle_other_deg 0.847 r_mcbond_it 0.748 r_symmetry_vdw_refined 0.288 r_symmetry_vdw_other 0.27 r_nbd_other 0.237 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.131 r_nbtor_other 0.084 r_chiral_restr 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3605 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing