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Crystal structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12 in complex with pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 298 100mM HEPES pH 6.5, 200mM MgCl2, 25% PEG 3350, Microbatch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.13 α = 90 b = 153.55 β = 90 c = 55.53 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.973 ESRF BM14
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 2.2 48.975 99.3 0.102 0.11 16.93 62107 -3 22.397
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) 2.2 2.25 96 0.339 0.37 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 2V8Z 2.2 48.975 62107 3106 100 0.181 0.179 0.1775 0.222 0.2195 RANDOM 13.778
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] -1.32 0.67 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.501 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 15.223 r_dihedral_angle_1_deg 6.064 r_scangle_it 3.906 r_scbond_it 2.53 r_angle_refined_deg 1.866 r_mcangle_it 1.375 r_mcbond_it 0.772 r_chiral_restr 0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.501 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 15.223 r_dihedral_angle_1_deg 6.064 r_scangle_it 3.906 r_scbond_it 2.53 r_angle_refined_deg 1.866 r_mcangle_it 1.375 r_mcbond_it 0.772 r_chiral_restr 0.189 r_bond_refined_d 0.023 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9055 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction