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3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with tryptophan and tyrosine bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NV8 PDB ENTRY 3NV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M TRIS-HCL PH 7.5, 1.5 M AMMONIUM SULFATE, 15% V/V GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.91 68.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.777 α = 90 b = 202.777 β = 90 c = 66.747 γ = 120
Symmetry Space Group P 32 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 RAXIS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2.8 39.72 99.2 0.13 7.2 4.06 39770 3
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 2.8 2.9 99.9 0.45 2.4 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-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 PDB ENTRY 3NV8 2.76 175.67 37979 1925 98.06 0.18081 0.1773 0.1988 0.24888 0.2541 RANDOM 34.809
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] -0.23 -0.23 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.614 r_dihedral_angle_4_deg 23.361 r_dihedral_angle_3_deg 22.967 r_dihedral_angle_1_deg 10.675 r_angle_refined_deg 3.348 r_angle_other_deg 1.494 r_chiral_restr 0.171 r_bond_refined_d 0.017 r_gen_planes_refined 0.016 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.614 r_dihedral_angle_4_deg 23.361 r_dihedral_angle_3_deg 22.967 r_dihedral_angle_1_deg 10.675 r_angle_refined_deg 3.348 r_angle_other_deg 1.494 r_chiral_restr 0.171 r_bond_refined_d 0.017 r_gen_planes_refined 0.016 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 7029 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction CrystalClear data scaling