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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 MANGANESE(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, 13-17MG/ML DAHPS
Crystal Properties Matthews coefficient Solvent content 1.94 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.636 α = 90 b = 50.502 β = 106.36 c = 64.93 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 2000-07-15 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 1.9 20 99.3 0.11 8.34 3.63 178093
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 1.9 1.95 97.5 0.38 2.9 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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1HFB 1.9 20 45985 2424 99.7 0.162 0.16 0.202 0.2059 RANDOM 16.98
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] 0.13 0.22 0.07 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.035 r_dihedral_angle_4_deg 18.204 r_dihedral_angle_3_deg 14.62 r_dihedral_angle_1_deg 5.868 r_scangle_it 5.207 r_scbond_it 3.32 r_angle_refined_deg 2.032 r_mcangle_it 1.878 r_mcbond_it 1.114 r_symmetry_hbond_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.035 r_dihedral_angle_4_deg 18.204 r_dihedral_angle_3_deg 14.62 r_dihedral_angle_1_deg 5.868 r_scangle_it 5.207 r_scbond_it 3.32 r_angle_refined_deg 2.032 r_mcangle_it 1.878 r_mcbond_it 1.114 r_symmetry_hbond_refined 0.319 r_chiral_restr 0.245 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.14 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 5160 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing