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Crystal structure of the complex of a hydroxyproline epimerase (TARGET EFI-506499, PSEUDOMONAS FLUORESCENS PF-5) with the inhibitor pyrrole-2-carboxylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AZP PDB entry 2AZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop vapor diffuction 5.6 298 Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 20 mM PYRROLE-2-CARBOXYLATE), Reservoir (0.17 M Ammonium Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5 %(w/v) PEG 4000, 15 %(v/v) Glycerol), Soak 2 minutes in (Reservoir + 20% Ethylene Glycol, 20 mM PYRROLE-2-CARBOXYLATE), sitting drop vapor diffuction, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.174 α = 90 b = 74.637 β = 105.46 c = 87.048 γ = 90
Symmetry Space Group P 1 21 1
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 MX225HE MIRRORS 2013-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-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 1.6 83.898 99.3 0.093 0.093 6.9 3.6 90740 90740
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 1.6 1.69 99.5 0.434 0.434 1.7 3.5 13196
Refinement Statistics Diffraction ID Structure Solution 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 2AZP 1.6 26.188 90665 90665 4552 99.24 0.1985 0.1985 0.1967 0.2318 0.2481 RANDOM 22.2842
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 14.747 f_angle_d 1.079 f_chiral_restr 0.078 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4708 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 36
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction AMoRE phasing