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Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADPH, 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, 100mM HEPES/NaOH pH 7.0, 200mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.894 α = 90 b = 70.455 β = 113.39 c = 122.052 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 2.85 50 92.4 0.087 7.6 2.7 44368
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 2.85 2.9 93.1 0.737 1.33 2.6
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 2.85 19.93 35802 1777 84.47 0.20265 0.19844 0.199 0.28774 0.2821 RANDOM 56.134
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] -0.3 -0.32 0.95 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.855 r_dihedral_angle_3_deg 20.297 r_dihedral_angle_4_deg 17.582 r_long_range_B_refined 7.723 r_long_range_B_other 7.723 r_dihedral_angle_1_deg 7.333 r_mcangle_it 4.775 r_mcangle_other 4.775 r_scangle_other 4.498 r_mcbond_it 2.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.855 r_dihedral_angle_3_deg 20.297 r_dihedral_angle_4_deg 17.582 r_long_range_B_refined 7.723 r_long_range_B_other 7.723 r_dihedral_angle_1_deg 7.333 r_mcangle_it 4.775 r_mcangle_other 4.775 r_scangle_other 4.498 r_mcbond_it 2.896 r_mcbond_other 2.895 r_scbond_it 2.66 r_scbond_other 2.66 r_angle_refined_deg 1.528 r_angle_other_deg 0.995 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 13090 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing