☰ Navigation Tabs
Crystal structures of Escherichia coli IspH in complex with AMBPP a potent inhibitor of the methylerythritol phosphate pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KE8 PDB ENTRY 3KE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 24% PEG 3350, 0.1 M BIS-TRIS PH6.5, 200 MM LISO4
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.12 α = 90 b = 80.65 β = 94.63 c = 71.09 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 225 mm CCD 2011-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.7 46.96 94.9 0.09 9.7 3.7 68152 2
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 1.7 1.8 94.6 0.4 2.8 3.7
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 3KE8 1.68 46.96 64744 3408 94.96 0.19001 0.18725 0.195 0.24179 0.2444 RANDOM 23.073
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] 2.57 0.27 -2.97 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.146 r_sphericity_free 20.899 r_dihedral_angle_4_deg 18.93 r_dihedral_angle_3_deg 14.227 r_rigid_bond_restr 12.069 r_sphericity_bonded 9.133 r_dihedral_angle_1_deg 5.216 r_angle_refined_deg 1.888 r_angle_other_deg 1.758 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.146 r_sphericity_free 20.899 r_dihedral_angle_4_deg 18.93 r_dihedral_angle_3_deg 14.227 r_rigid_bond_restr 12.069 r_sphericity_bonded 9.133 r_dihedral_angle_1_deg 5.216 r_angle_refined_deg 1.888 r_angle_other_deg 1.758 r_chiral_restr 0.131 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4753 Nucleic Acid Atoms Solvent Atoms 809 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing