☰ Navigation Tabs
Inhibitors of the herbicidal target IspD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YC3 PDB ENTRY 2YC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 NATIVE CRYSTALS (SEE REMARK 1, PDB 1W77) WERE SOAKED WITH A SATURATED SOLUTION OF LIGAND
Crystal Properties Matthews coefficient Solvent content 2.15 42.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.9 α = 90 b = 74.9 β = 90 c = 220.06 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 CCD MARMOSAIC 225 mm CCD 2006-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 1.6 26.1 99.8 0.08 14.21 5.5 31753 -3 29.1
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 1.6 1.7 99.9 0.73 2.59 5
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 2YC3 1.6 26.11 30161 1587 99.77 0.15234 0.15037 0.1615 0.18897 0.1941 RANDOM 22.157
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] -0.11 -0.05 -0.11 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.615 r_dihedral_angle_3_deg 15.692 r_dihedral_angle_4_deg 10.949 r_scangle_it 8.149 r_dihedral_angle_1_deg 6.056 r_scbond_it 5.478 r_mcangle_it 3.607 r_mcbond_it 2.335 r_rigid_bond_restr 2.213 r_angle_refined_deg 2.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.615 r_dihedral_angle_3_deg 15.692 r_dihedral_angle_4_deg 10.949 r_scangle_it 8.149 r_dihedral_angle_1_deg 6.056 r_scbond_it 5.478 r_mcangle_it 3.607 r_mcbond_it 2.335 r_rigid_bond_restr 2.213 r_angle_refined_deg 2.075 r_angle_other_deg 1.15 r_mcbond_other 0.944 r_chiral_restr 0.143 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 1698 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing