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crystal structure of the tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae complexed with tyrosine and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HFB MOLECULE A OF PDB-CODE 1HFB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 pH 8.00
Crystal Properties Matthews coefficient Solvent content 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.129 α = 64.71 b = 94.696 β = 85.51 c = 104.843 γ = 75.61
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 2001-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 2.05 20 96.5 0.067 10.1 2.4 407127 2.05
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 2.05 2.1 89.1 0.28 2.1 1.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT MOLECULE A OF PDB-CODE 1HFB 2.1 20 151729 4949 97.2 0.195 0.237 0.2459 RANDOM 43.66
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.931 r_scangle_it 4.444 r_angle_other_deg 3.888 r_scbond_it 2.807 r_angle_refined_deg 1.996 r_mcangle_it 1.856 r_mcbond_it 1.064 r_symmetry_hbond_refined 0.372 r_nbd_other 0.279 r_symmetry_vdw_other 0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.931 r_scangle_it 4.444 r_angle_other_deg 3.888 r_scbond_it 2.807 r_angle_refined_deg 1.996 r_mcangle_it 1.856 r_mcbond_it 1.064 r_symmetry_hbond_refined 0.372 r_nbd_other 0.279 r_symmetry_vdw_other 0.274 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.12 r_nbtor_other 0.114 r_bond_refined_d 0.024 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 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 20826 Nucleic Acid Atoms Solvent Atoms 667 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing