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Development of Alkyl Glycerone Phosphate Synthase Inhibitors: Complex with Inhibitor 2I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ADZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 PEG 1500 20%, HEPES, PH 7.5, 100 MM
Crystal Properties Matthews coefficient Solvent content 2.26 45.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.958 α = 90 b = 120.644 β = 95.27 c = 148.16 γ = 90
Symmetry Space Group I 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 PIXEL DECTRIS PILATUS 300K 2015-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.8729 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.9 48 100 0.181 0.994 11.2 7.8 57552
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.98 100 0.8 0.826 2.9 8.1
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 FOURIER SYNTHESIS THROUGHOUT 5ADZ 2.9 48 54617 2934 99.97 0.22057 0.21858 0.2207 0.25817 0.2581 RANDOM 48.02
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] -0.89 -1.93 2.42 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.683 r_dihedral_angle_3_deg 16.939 r_dihedral_angle_4_deg 16.315 r_long_range_B_refined 8.22 r_long_range_B_other 8.22 r_dihedral_angle_1_deg 6.363 r_scangle_other 5.474 r_mcangle_it 5.427 r_mcangle_other 5.427 r_mcbond_it 3.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.683 r_dihedral_angle_3_deg 16.939 r_dihedral_angle_4_deg 16.315 r_long_range_B_refined 8.22 r_long_range_B_other 8.22 r_dihedral_angle_1_deg 6.363 r_scangle_other 5.474 r_mcangle_it 5.427 r_mcangle_other 5.427 r_mcbond_it 3.367 r_mcbond_other 3.366 r_scbond_it 3.289 r_scbond_other 3.289 r_angle_refined_deg 1.456 r_angle_other_deg 1.223 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17058 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 287
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling REFMAC phasing