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Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (UDP-N-acetylglucosamine enolpyruvyl transferase, EPT) from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VCY PDB entry 3vcy modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 Microlytics MCSG1 A11: 10% PEG 4000, 200mM MgCl2, 100mM MES/NaOH pH 6.5, PsaeA.00952.a.B1.PS02212 at 17mg/ml + 3mM UDP-N-acetylglucosamine + 3mM phosphoenolpyruvate, cryo: 20% EG in 2 steps; tray 260011a11, puck fvw9-7
Crystal Properties Matthews coefficient Solvent content 2.42 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.17 α = 90 b = 166.81 β = 90 c = 81.45 γ = 90
Symmetry Space Group P 21 21 2
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-225 2015-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.7 50 99.3 0.083 0.095 12.07 4 194666 193295 -3 13
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 1.7 1.74 99.7 0.459 0.526 2.88 4.1
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 PDB entry 3vcy modified with CCP4 program CHAINSAW 1.7 43.414 1.36 193266 9570 99.29 0.1501 0.1484 0.1509 0.1809 0.1826 Random selection 17.1776
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 12.6 f_angle_d 1.169 f_chiral_restr 0.051 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12630 Nucleic Acid Atoms Solvent Atoms 2060 Heterogen Atoms 182
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing ARP model building Coot model building PHENIX refinement