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The structure of wt A. thaliana IGPD2 in complex with Mn2+ and formate at 1.3A 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 8.5 290 14% PEG200, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.77 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.15 α = 90 b = 114.15 β = 90 c = 114.15 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 2010-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 30.51 99.2 0.064 13.9 6.6 62158 62158
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 1.37 97.7 0.574 3 6.8 8754
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 26.91 62158 58902 3119 98.74 0.13344 0.13291 0.1315 0.14355 0.1427 RANDOM 17.506
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 32.572 r_sphericity_free 26.518 r_sphericity_bonded 23.476 r_dihedral_angle_4_deg 17.199 r_rigid_bond_restr 13.328 r_dihedral_angle_3_deg 12.867 r_dihedral_angle_1_deg 6.558 r_scbond_it 6.375 r_scbond_other 6.375 r_scangle_other 5.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.572 r_sphericity_free 26.518 r_sphericity_bonded 23.476 r_dihedral_angle_4_deg 17.199 r_rigid_bond_restr 13.328 r_dihedral_angle_3_deg 12.867 r_dihedral_angle_1_deg 6.558 r_scbond_it 6.375 r_scbond_other 6.375 r_scangle_other 5.566 r_long_range_B_refined 5.268 r_long_range_B_other 5.092 r_mcangle_other 2.798 r_mcangle_it 2.745 r_mcbond_it 2.472 r_mcbond_other 2.472 r_angle_refined_deg 1.504 r_angle_other_deg 1.375 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 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 1433 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 14
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling