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The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in complex with phosphoenol pyruvate and manganese (thesit-free)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KGF 3KGF (stripped of ligands and waters)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 20MM BTP, 150MM NACL, 0.5MM TCEP, 0.2MM PEP, 0.1MM MNCL2, 0.1M HEPES, 0.8M NAK PHOSPHATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.91 68.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.538 α = 90 b = 203.538 β = 90 c = 66.422 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 120 IMAGE PLATE RIGAKU RAXIS IV++ AXCO PX70 2009-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.25 39.4 97.2 0.118 8.3 6.1 73037 73037 33
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 2.25 2.33 95.4 0.434 3.4 6.11 7137
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 3KGF (stripped of ligands and waters) 2.25 39.37 69535 3648 97.41 0.18137 0.17997 0.208 0.1994 RANDOM 36.915
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] -0.18 -0.09 -0.18 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.064 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_3_deg 17.497 r_dihedral_angle_1_deg 7.335 r_scangle_it 4.267 r_scbond_it 2.991 r_angle_refined_deg 2.157 r_mcangle_it 1.963 r_mcbond_it 1.181 r_angle_other_deg 1.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.064 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_3_deg 17.497 r_dihedral_angle_1_deg 7.335 r_scangle_it 4.267 r_scbond_it 2.991 r_angle_refined_deg 2.157 r_mcangle_it 1.963 r_mcbond_it 1.181 r_angle_other_deg 1.148 r_mcbond_other 0.32 r_chiral_restr 0.126 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_gen_planes_other 0.001 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7098 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 69
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling