☰ Navigation Tabs
The form B structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and its substrate, 2R3S-IGP, to 1.41 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 7 290 0.05% PEG2000, 0.4 M succinic acid, pH 7.0, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.9 α = 90 b = 112.9 β = 90 c = 112.9 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 PIXEL DECTRIS PILATUS 6M two K-B pairs of bimorph type mirrors 2011-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.41 65.183 100 0.085 17.7 10.5 47547 47547 12.197
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 1.41 1.45 100 0.849 3.4 10.8 3450
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2F1D 1.41 65.183 47547 45244 2303 99.93 0.12495 0.12347 0.1536 0.1557 RANDOM 17.769
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 35.447 r_sphericity_bonded 32.863 r_dihedral_angle_2_deg 31.967 r_dihedral_angle_4_deg 14.888 r_rigid_bond_restr 12.77 r_dihedral_angle_3_deg 10.984 r_scbond_it 7.915 r_scbond_other 7.91 r_scangle_other 7.09 r_long_range_B_other 6.838
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.447 r_sphericity_bonded 32.863 r_dihedral_angle_2_deg 31.967 r_dihedral_angle_4_deg 14.888 r_rigid_bond_restr 12.77 r_dihedral_angle_3_deg 10.984 r_scbond_it 7.915 r_scbond_other 7.91 r_scangle_other 7.09 r_long_range_B_other 6.838 r_long_range_B_refined 6.829 r_dihedral_angle_1_deg 6.502 r_mcangle_other 5.416 r_mcangle_it 5.415 r_mcbond_it 5.017 r_mcbond_other 5.01 r_angle_refined_deg 1.497 r_angle_other_deg 0.821 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 196 Heterogen Atoms 29
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling SCALA data scaling