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Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 100MM BIS-TRIS PH 5.5, 200MM MGCL2, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.279 α = 90 b = 149.806 β = 108.42 c = 78.967 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 ADSC CCD 2006-12-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9794 , 0.9796 , 0.9762 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 99.9 0.06 19 7.5 67391 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 99.7 0.14 7.4
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 MAD THROUGHOUT NONE 2.15 36.35 63872 3466 99.7 0.168 0.166 0.1661 0.218 0.2162 RANDOM 15.53
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 r_dihedral_angle_2_deg 37.185 r_dihedral_angle_4_deg 19.738 r_dihedral_angle_3_deg 15.33 r_dihedral_angle_1_deg 10.653 r_scangle_it 3.808 r_scbond_it 2.701 r_angle_refined_deg 1.682 r_mcangle_it 1.358 r_mcbond_it 0.987 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.185 r_dihedral_angle_4_deg 19.738 r_dihedral_angle_3_deg 15.33 r_dihedral_angle_1_deg 10.653 r_scangle_it 3.808 r_scbond_it 2.701 r_angle_refined_deg 1.682 r_mcangle_it 1.358 r_mcbond_it 0.987 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.241 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.128 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9011 Nucleic Acid Atoms Solvent Atoms 649 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing PHENIX phasing