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The structure of wt A. thaliana IGPD2 in complex with Mn2+ and 1,2,4-triazole at 1.3 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 9 290 30% PEG200, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.13 α = 90 b = 113.13 β = 90 c = 113.13 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 1.3 50.59 100 0.053 25.2 12.3 61097 61097 12.36
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 1.3 1.33 99.9 0.762 3.5 12.5 4421
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 1.3 50.59 61097 58015 3072 99.88 0.13049 0.12956 0.1263 0.14806 0.1443 RANDOM 19.128
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_bonded 35.322 r_dihedral_angle_2_deg 30.94 r_sphericity_free 25.551 r_dihedral_angle_4_deg 15.992 r_rigid_bond_restr 13.402 r_dihedral_angle_3_deg 10.415 r_scbond_other 9.539 r_scbond_it 9.533 r_dihedral_angle_1_deg 6.604 r_scangle_other 6.07
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 35.322 r_dihedral_angle_2_deg 30.94 r_sphericity_free 25.551 r_dihedral_angle_4_deg 15.992 r_rigid_bond_restr 13.402 r_dihedral_angle_3_deg 10.415 r_scbond_other 9.539 r_scbond_it 9.533 r_dihedral_angle_1_deg 6.604 r_scangle_other 6.07 r_long_range_B_other 5.637 r_long_range_B_refined 5.635 r_mcangle_other 2.027 r_mcangle_it 1.931 r_mcbond_it 1.747 r_angle_refined_deg 1.525 r_mcbond_other 1.52 r_angle_other_deg 0.852 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1439 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 24
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling SCALA data scaling