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Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (HTPA reductase) from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ARZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 Morpheus D9: 20mM of each: 1,6-Hexanediol; 1-Butanol, 1,2-Propanediol (racemic); 2-Propanol; 1,4-Butanediol; 1,3-Propanediol; 100mM Tris Base / Bicine pH 8.5, 30% each PEG 550MME, PEG 20000; PsaeA.00820.a.B1.PW37541 at 22.65 mg/ml; cryo: direct; tray 259740d90, puck hxm4-4
Crystal Properties Matthews coefficient Solvent content 2.91 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.01 α = 90 b = 101.5 β = 90 c = 144.51 γ = 90
Symmetry Space Group C 2 2 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 RAYONIX MX-300 2014-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978560 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.8 50 99.4 0.048 0.053 18.11 5 63326 -3 24.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 100 0.517 0.578 2.9 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE 1ARZ 1.8 34.287 1.34 62927 3153 99.1 0.1694 0.1677 0.1683 0.2006 0.2008 Random selection 36.7854
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.896 f_angle_d 0.991 f_chiral_restr 0.048 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3872 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 121
Software Software Software Name Purpose XDS data reduction PHASER phasing ARP model building Coot model building PHENIX refinement PDB_EXTRACT data extraction XSCALE data scaling