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Crystal structure of the tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae in complex with phosphoenolpyruvate and cobalt(ii)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HFB PDB ENTRY 1HFB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 TRIS PH 7.5-9.0 10 MM 20% PEG3400, 5% GLYCEROL, 4 EQUIV. PEP, 2.5 EQUIV. CO2+ 13-17MG/ML DAHPS
Crystal Properties Matthews coefficient Solvent content 1.94 36.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.21 α = 90 b = 50.61 β = 106.33 c = 64.98 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE MARRESEARCH MIRRORS 2000-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 2.02 18.6 96.8 0.053 15.1 3.2 128877
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 2.02 2.15 86.8 0.28 3.5 2
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1HFB 2.02 17.57 37403 1971 97.1 0.155 0.1615 0.204 0.2109 RANDOM 24.18
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.447 r_scangle_it 5.643 r_scbond_it 3.726 r_angle_other_deg 3.669 r_angle_refined_deg 2.305 r_mcangle_it 2.102 r_mcbond_it 1.241 r_symmetry_vdw_other 0.339 r_nbd_other 0.302 r_chiral_restr 0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.447 r_scangle_it 5.643 r_scbond_it 3.726 r_angle_other_deg 3.669 r_angle_refined_deg 2.305 r_mcangle_it 2.102 r_mcbond_it 1.241 r_symmetry_vdw_other 0.339 r_nbd_other 0.302 r_chiral_restr 0.274 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.216 r_symmetry_hbond_refined 0.213 r_xyhbond_nbd_refined 0.174 r_nbtor_other 0.112 r_bond_refined_d 0.031 r_gen_planes_other 0.015 r_gen_planes_refined 0.01 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 5152 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing