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A. thaliana IGPD2 in complex with the racemate of the triazole-phosphonate inhibitor, C348
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QNK
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 550 MME
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.905 α = 90 b = 112.905 β = 90 c = 112.905 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 2009-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.95070 Diamond I03
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 1.1 35.7 99.5 0.082 15.1 10.6 98895 98895
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 1.1 1.12 98.3 0.676 2.2 5.1
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 MOLECULAR REPLACEMENT THROUGHOUT 4QNK 1.1 35.7 93872 4953 99.4 0.12394 0.12348 0.1226 0.13258 0.1314 RANDOM 15.171
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 34.731 r_sphericity_free 25.219 r_dihedral_angle_4_deg 16.994 r_sphericity_bonded 16.514 r_dihedral_angle_3_deg 10.731 r_rigid_bond_restr 9.622 r_dihedral_angle_1_deg 6.645 r_long_range_B_other 5.55 r_long_range_B_refined 5.546 r_scangle_other 5.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.731 r_sphericity_free 25.219 r_dihedral_angle_4_deg 16.994 r_sphericity_bonded 16.514 r_dihedral_angle_3_deg 10.731 r_rigid_bond_restr 9.622 r_dihedral_angle_1_deg 6.645 r_long_range_B_other 5.55 r_long_range_B_refined 5.546 r_scangle_other 5.334 r_scbond_it 5.144 r_scbond_other 5.14 r_mcangle_it 2.9 r_mcangle_other 2.899 r_mcbond_other 2.577 r_mcbond_it 2.575 r_angle_refined_deg 1.793 r_angle_other_deg 1.586 r_chiral_restr 0.101 r_bond_refined_d 0.01 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 1494 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling REFMAC phasing