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Crystal structure of DAH7PS-CM complex from Geobacillus sp. with prephenate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 298 A protein solution (11 mg/mL in 20 mM BTP, 40 mM KCl, 200 ??M PEP, pH 7.4) was mixed 1:1 (v/v)
with a reservoir solution containing 0.2 M sodium citrate, 0.1 M BTP, pH 6.5, 20% W/V PEG 3350 and 0.2 mM chorismic acid. 2 ??L drop size. 500 ??L reservoir volume.
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.438 α = 90 b = 95.438 β = 90 c = 167.452 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 110 CCD ADSC QUANTUM 315r 2012-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953700 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.75 82.65 99.9 0.079 1 18 7.6 22482
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 2.75 2.88 100 1.336 7.7
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 MOLECULAR REPLACEMENT THROUGHOUT 3TFC 2.75 82.65 21178 1054 99.02 0.18471 0.18221 0.1865 0.2352 0.2319 RANDOM 77.759
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] -0.49 -0.24 -0.49 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.677 r_dihedral_angle_3_deg 18.841 r_dihedral_angle_4_deg 16.568 r_long_range_B_other 7.983 r_long_range_B_refined 7.981 r_dihedral_angle_1_deg 6.922 r_scangle_other 6.26 r_mcangle_it 4.289 r_mcangle_other 4.289 r_scbond_it 3.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.677 r_dihedral_angle_3_deg 18.841 r_dihedral_angle_4_deg 16.568 r_long_range_B_other 7.983 r_long_range_B_refined 7.981 r_dihedral_angle_1_deg 6.922 r_scangle_other 6.26 r_mcangle_it 4.289 r_mcangle_other 4.289 r_scbond_it 3.895 r_scbond_other 3.894 r_mcbond_it 2.729 r_mcbond_other 2.726 r_angle_refined_deg 2.12 r_angle_other_deg 1.511 r_chiral_restr 0.107 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.007 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 5366 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction