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Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADH, alpha-ketoglutarate and ca2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AJ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20% PEG 6000, 100 mM HEPES/NaOH pH 7.0, 200mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.54 51.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.52 α = 90 b = 70.464 β = 113.42 c = 121.929 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX300HE 2016-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 2.9 50 93.8 0.098 5.7 2.4 39505
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 2.9 2.95 89.2 0.692 1.03 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 6AJ6 2.9 19.98 32695 1741 81.9 0.19645 0.19178 0.1933 0.28356 0.2791 RANDOM 56.642
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] 0.06 0.25 -0.54 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.404 r_dihedral_angle_3_deg 22.193 r_dihedral_angle_4_deg 20.418 r_dihedral_angle_1_deg 8.52 r_long_range_B_other 5.074 r_long_range_B_refined 5.073 r_mcangle_it 3.025 r_mcangle_other 3.025 r_scangle_other 2.876 r_angle_refined_deg 1.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.404 r_dihedral_angle_3_deg 22.193 r_dihedral_angle_4_deg 20.418 r_dihedral_angle_1_deg 8.52 r_long_range_B_other 5.074 r_long_range_B_refined 5.073 r_mcangle_it 3.025 r_mcangle_other 3.025 r_scangle_other 2.876 r_angle_refined_deg 1.898 r_mcbond_it 1.761 r_mcbond_other 1.761 r_scbond_it 1.652 r_scbond_other 1.652 r_angle_other_deg 1.114 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13048 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing