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The structure of wt A. thaliana IGPD2 in complex with Mn2+, imidazole, and sulfate at 1.5 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, SITTING DROP 8 290 10% PEG3000, 0.2 M lithium sulfate, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.6 52.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.88 α = 90 b = 113.88 β = 90 c = 113.88 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 2008-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9507 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 1.5 40.26 99.2 0.053 31.8 12.8 40587 40587 12.651
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 1.5 1.54 100 0.676 4 12.2 2956
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 1.5 40.26 40587 38579 2008 99.09 0.15958 0.15806 0.18832 0.1796 RANDOM 22.688
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 37.715 r_sphericity_bonded 35.302 r_dihedral_angle_2_deg 30.512 r_rigid_bond_restr 13.947 r_dihedral_angle_4_deg 13.411 r_dihedral_angle_3_deg 10.56 r_scbond_other 9.886 r_scbond_it 9.881 r_scangle_other 9.304 r_long_range_B_refined 7.129
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.715 r_sphericity_bonded 35.302 r_dihedral_angle_2_deg 30.512 r_rigid_bond_restr 13.947 r_dihedral_angle_4_deg 13.411 r_dihedral_angle_3_deg 10.56 r_scbond_other 9.886 r_scbond_it 9.881 r_scangle_other 9.304 r_long_range_B_refined 7.129 r_long_range_B_other 7.127 r_dihedral_angle_1_deg 6.593 r_mcangle_other 3.399 r_mcangle_it 3.271 r_mcbond_it 3.159 r_mcbond_other 2.848 r_angle_refined_deg 1.571 r_angle_other_deg 0.975 r_chiral_restr 0.103 r_bond_refined_d 0.013 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 1439 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 29
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling SCALA data scaling