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The form A structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and a mixture of its substrate, 2R3S-IGP, and an inhibitor, 2S3S-IGP, to 1.12 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F1D PDB ENTRY 2F1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 290 25% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.69 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.1 α = 90 b = 113.1 β = 90 c = 113.1 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 Kirkpatrick Baez bimorph mirror pair 2011-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9794 Diamond I02
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 1.12 46.17 99.1 0.041 30.8 9.5 94992 94992
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 1.12 1.14 93.9 0.568 2.5 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2F1D 1.12 46.17 94992 89279 4612 99.08 0.12577 0.12511 0.1234 0.13856 0.1381 RANDOM 16.019
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_sphericity_free 38.849 r_sphericity_bonded 34.042 r_dihedral_angle_2_deg 32.133 r_rigid_bond_restr 18.34 r_dihedral_angle_4_deg 12.548 r_dihedral_angle_3_deg 10.447 r_scbond_it 10.287 r_scbond_other 10.247 r_scangle_other 8.807 r_dihedral_angle_1_deg 6.576
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.849 r_sphericity_bonded 34.042 r_dihedral_angle_2_deg 32.133 r_rigid_bond_restr 18.34 r_dihedral_angle_4_deg 12.548 r_dihedral_angle_3_deg 10.447 r_scbond_it 10.287 r_scbond_other 10.247 r_scangle_other 8.807 r_dihedral_angle_1_deg 6.576 r_long_range_B_refined 6.338 r_long_range_B_other 6.336 r_mcbond_other 2.321 r_mcbond_it 2.318 r_mcangle_other 1.736 r_mcangle_it 1.725 r_angle_refined_deg 1.715 r_angle_other_deg 0.876 r_chiral_restr 0.112 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1443 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 52
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling SCALA data scaling