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A. thaliana IGPD2 in complex with the triazole-phosphonate inhibitor, (R)-C348, to 1.36A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 0.1M Tris-HCl pH8.5 and 20% PEG 300
Crystal Properties Matthews coefficient Solvent content 2.66 53.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.58 α = 90 b = 112.58 β = 90 c = 112.58 γ = 90
Symmetry Space Group P 4 3 2
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 ADSC QUANTUM 315 2010-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98020 Diamond I04
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 1.36 45.96 99 0.068 23.8 9.1 52156 52156
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 1.36 1.4 89.1 0.66 2.8 7.5
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 5EKW 1.4 45.96 47188 1225 99.8 0.1172 0.11666 0.1161 0.1312 0.1318 RANDOM 11.722
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.662 r_sphericity_free 20.309 r_dihedral_angle_4_deg 18.546 r_dihedral_angle_3_deg 10.885 r_sphericity_bonded 10.108 r_rigid_bond_restr 8.409 r_dihedral_angle_1_deg 6.604 r_scbond_other 2.9 r_scbond_it 2.898 r_long_range_B_refined 2.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.662 r_sphericity_free 20.309 r_dihedral_angle_4_deg 18.546 r_dihedral_angle_3_deg 10.885 r_sphericity_bonded 10.108 r_rigid_bond_restr 8.409 r_dihedral_angle_1_deg 6.604 r_scbond_other 2.9 r_scbond_it 2.898 r_long_range_B_refined 2.434 r_long_range_B_other 2.433 r_scangle_other 2.37 r_angle_other_deg 1.825 r_angle_refined_deg 1.59 r_mcangle_other 1.111 r_mcangle_it 1.108 r_mcbond_it 0.942 r_mcbond_other 0.931 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1533 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing