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Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - SeMet protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 100 MM TRIS-HCL PH 8.5, 22 % PEG 8K, 15 % GLYCEROL, 200 MM NACL
Crystal Properties Matthews coefficient Solvent content 2.5 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.83 α = 90 b = 95.83 β = 90 c = 463.17 γ = 120
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 2007-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.8 83 99.5 0.1 20.6 10.3 57944 40.8
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 2.8 2.88 96.8 0.26 6.4 6.7
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 SAD THROUGHOUT NONE 2.81 83.05 54880 2936 99.5 0.172 0.169 0.17 0.233 0.2298 RANDOM 19.85
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] 1.39 0.69 1.39 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.999 r_dihedral_angle_4_deg 22.323 r_dihedral_angle_3_deg 18.936 r_dihedral_angle_1_deg 6.898 r_scangle_it 1.979 r_angle_refined_deg 1.353 r_scbond_it 1.173 r_mcangle_it 0.658 r_mcbond_it 0.327 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.999 r_dihedral_angle_4_deg 22.323 r_dihedral_angle_3_deg 18.936 r_dihedral_angle_1_deg 6.898 r_scangle_it 1.979 r_angle_refined_deg 1.353 r_scbond_it 1.173 r_mcangle_it 0.658 r_mcbond_it 0.327 r_chiral_restr 0.097 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 17324 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling SOLVE phasing