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Inhibitors of the herbicidal target IspD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W77 PDB ENTRY 1W77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 NATIVE CRYSTALS (SEE REMARK 1, PDB 1W77) WERE SOAKED WITH A SATURATED SOLUTION OF LIGAND MW5
Crystal Properties Matthews coefficient Solvent content 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.6 α = 90 b = 74.6 β = 90 c = 220.5 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PILATUS 6M 2005-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.4 37.3 99.7 0.1 16.96 11 48851 26.5
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 1.4 1.45 99.1 0.84 2.58 8
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 1W77 1.4 37.3 44478 2372 99.7 0.16454 0.16248 0.1699 0.20408 0.2041 RANDOM 20.138
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.018 r_dihedral_angle_4_deg 17.055 r_dihedral_angle_3_deg 13.717 r_scangle_it 7.387 r_dihedral_angle_1_deg 6.128 r_scbond_it 5.243 r_mcangle_it 3.661 r_mcbond_it 2.548 r_rigid_bond_restr 2.337 r_angle_refined_deg 2.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.018 r_dihedral_angle_4_deg 17.055 r_dihedral_angle_3_deg 13.717 r_scangle_it 7.387 r_dihedral_angle_1_deg 6.128 r_scbond_it 5.243 r_mcangle_it 3.661 r_mcbond_it 2.548 r_rigid_bond_restr 2.337 r_angle_refined_deg 2.206 r_angle_other_deg 1.132 r_mcbond_other 1.037 r_chiral_restr 0.15 r_bond_refined_d 0.028 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1710 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing