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Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QR7 CHIMERIC MODEL FROM 1QR7 AND 1FWT experimental model PDB 1FWT CHIMERIC MODEL FROM 1QR7 AND 1FWT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 295 8% Peg 8000, 0.2M ammonium acetate, 0.1M tris-HCl, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.231 α = 90 b = 110.024 β = 90 c = 144.35 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV Osmic Blue Mirrors 2004-05-07 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 19.8 99.9 0.126 7.6 4.97 166567 33241 30.1
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 2.37 100 0.35 3.9 4.97
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 CHIMERIC MODEL FROM 1QR7 AND 1FWT 2.25 19.8 30722 30722 2519 100 0.186 0.18224 0.1925 0.23132 0.2394 RANDOM 31.545
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] 0.45 1.72 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.654 r_scangle_it 5.405 r_scbond_it 3.68 r_mcangle_it 2.693 r_mcbond_it 1.613 r_angle_refined_deg 1.563 r_angle_other_deg 1.562 r_symmetry_hbond_refined 0.264 r_nbd_other 0.257 r_symmetry_vdw_other 0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.654 r_scangle_it 5.405 r_scbond_it 3.68 r_mcangle_it 2.693 r_mcbond_it 1.613 r_angle_refined_deg 1.563 r_angle_other_deg 1.562 r_symmetry_hbond_refined 0.264 r_nbd_other 0.257 r_symmetry_vdw_other 0.253 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.237 r_xyhbond_nbd_refined 0.213 r_chiral_restr 0.093 r_nbtor_other 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4112 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 23
Software Software Software Name Purpose CrystalClear data collection CrystalClear data reduction MOLREP phasing REFMAC refinement CrystalClear data scaling