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Crystal Structure of the Tyrosine Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae in Complex with 2-Phosphoglycolate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HFB PDB ENTRY 1HFB (MOLECULE A)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8.00
Crystal Properties Matthews coefficient Solvent content 1.96 37.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.457 α = 90 b = 50.955 β = 106.41 c = 64.976 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 100 IMAGE PLATE MARRESEARCH MIRRORS 2001-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ROTATING ANODE (CU)
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 1.86 17.3 95.4 0.0444 19.77 3.8 198507
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 1.86 1.95 89.1 0.3035 4.36 3.1
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 (MOLECULE A) 1.86 17.3 47358 2493 95.6 0.165 0.1709 0.209 0.2171 RANDOM 25.62
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 5.808 r_scangle_it 5.015 r_angle_other_deg 3.705 r_scbond_it 3.114 r_mcangle_it 1.871 r_angle_refined_deg 1.728 r_mcbond_it 1.047 r_nbd_other 0.292 r_symmetry_vdw_other 0.285 r_nbd_refined 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.808 r_scangle_it 5.015 r_angle_other_deg 3.705 r_scbond_it 3.114 r_mcangle_it 1.871 r_angle_refined_deg 1.728 r_mcbond_it 1.047 r_nbd_other 0.292 r_symmetry_vdw_other 0.285 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.223 r_chiral_restr 0.136 r_xyhbond_nbd_refined 0.134 r_symmetry_vdw_refined 0.116 r_nbtor_other 0.108 r_bond_refined_d 0.02 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 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 5165 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing