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Non-covalent complex of and DAHP synthase and chorismate mutase from Corynebacterium glutamicum with bound transition state analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM imidazole/MES buffer, pH 6.5
30 mM each of ethylene glycol mix (di-ethylene glycol, tri-ethylene glycol, tetra-ethylene glycol, penta-ethylene glycol)
15% glycerol
15% PEG 4000
micro-seeded from badly diffracting crystals (approx. 8 AA resolution), in 100 mM Na-HEPES, pH 7.5, 200 mM LiSO4, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.45 64.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.622 α = 90 b = 110.481 β = 101.41 c = 134.652 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 PIXEL DECTRIS PILATUS 6M 2015-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97239 ESRF ID29
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 2.1 131.99 96.7 0.199 4.79 2.95 190339
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 2.1 2.23 85.7 1.763 0.44 2.24
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 2W1A 2.15 40 170847 8846 97.99 0.25191 0.24952 0.253 0.298 0.3001 RANDOM 33.789
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] 0.57 0.09 -1.03 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.924 r_dihedral_angle_3_deg 16.337 r_dihedral_angle_4_deg 16.187 r_dihedral_angle_1_deg 6.091 r_long_range_B_refined 5.8 r_long_range_B_other 5.8 r_scangle_other 3.552 r_mcangle_it 3.154 r_mcangle_other 3.154 r_scbond_it 2.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.924 r_dihedral_angle_3_deg 16.337 r_dihedral_angle_4_deg 16.187 r_dihedral_angle_1_deg 6.091 r_long_range_B_refined 5.8 r_long_range_B_other 5.8 r_scangle_other 3.552 r_mcangle_it 3.154 r_mcangle_other 3.154 r_scbond_it 2.165 r_scbond_other 2.165 r_mcbond_it 1.926 r_mcbond_other 1.926 r_angle_refined_deg 1.531 r_angle_other_deg 0.986 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16558 Nucleic Acid Atoms Solvent Atoms 779 Heterogen Atoms 871
Software Software Software Name Purpose REFMAC refinement PHASER phasing Aimless data scaling XDS data scaling XDS data reduction