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Structure the proline utilization A proline dehydrogenase domain (PutA86-630) inactivated with N-propargylglycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TIW pdb entry 1tiw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 The reservoir contained three parts of reagent A and one part of reagent B. Reagent A consists of 26% (w/v) PEG 5000 MME, 0.15 M ammonium sulfate, and 0.1 M MES at pH 5.8. Reagent B consists of 0.2 M MgCl2, 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.48 α = 90 b = 133.36 β = 90 c = 133.64 γ = 90
Symmetry Space Group I 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD NOIR-1 2007-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00000 ALS 4.2.2
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 2.15 31.409 97.9 0.094 0.094 10.3 4 60418
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) 2.15 2.27 98.9 0.489 0.489 1.4 3.3 8840
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT pdb entry 1tiw 2.15 30.748 1.35 60403 3048 97.39 0.195 0.193 0.1892 0.234 0.2297 RANDOM 33.85
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] -1.213 2.815 -1.601
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.964 f_angle_d 0.982 f_chiral_restr 0.061 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6133 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 106
Software Software Software Name Purpose SCALA data processing PHENIX refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction SCALA data scaling MOLREP phasing