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Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed 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 3000, 60-190mM citrate buffer, 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 = 72.814 α = 90 b = 141.124 β = 90 c = 146.015 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 99 98 0.076 0.076 23 5.9 51161 50059 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 2.07 91 0.469 0.469 2.1 4.4 4618
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 40.49 50055 47562 2493 98 0.216 0.2161 0.2141 0.2213 0.25522 0.2629 RANDOM 29.148
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] 0.45 3.66 -4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.533 r_scangle_it 3.466 r_scbond_it 2.174 r_angle_refined_deg 1.403 r_mcangle_it 1.372 r_angle_other_deg 0.838 r_mcbond_it 0.732 r_symmetry_vdw_other 0.287 r_nbd_other 0.236 r_nbd_refined 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.533 r_scangle_it 3.466 r_scbond_it 2.174 r_angle_refined_deg 1.403 r_mcangle_it 1.372 r_angle_other_deg 0.838 r_mcbond_it 0.732 r_symmetry_vdw_other 0.287 r_nbd_other 0.236 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.105 r_nbtor_other 0.084 r_chiral_restr 0.08 r_bond_refined_d 0.014 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 3474 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing