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Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADP+, 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 25% PEG 1500, 100mM PCB buffer
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.474 α = 90 b = 112.021 β = 90 c = 132.136 γ = 90
Symmetry Space Group P 21 21 21
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 2016-04-18 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 2.4 50 98.9 0.059 9.6 3.6 34871
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 2.4 2.44 98.6 0.544 1.9 3.3
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 2.4 20 30973 1596 93.71 0.21939 0.21671 0.2219 0.27058 0.2777 RANDOM 51.845
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] -1 0.83 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.164 r_dihedral_angle_4_deg 21.106 r_dihedral_angle_3_deg 20.576 r_dihedral_angle_1_deg 7.564 r_long_range_B_refined 4.242 r_long_range_B_other 4.172 r_angle_refined_deg 1.67 r_mcangle_it 1.666 r_mcangle_other 1.665 r_scangle_other 1.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.164 r_dihedral_angle_4_deg 21.106 r_dihedral_angle_3_deg 20.576 r_dihedral_angle_1_deg 7.564 r_long_range_B_refined 4.242 r_long_range_B_other 4.172 r_angle_refined_deg 1.67 r_mcangle_it 1.666 r_mcangle_other 1.665 r_scangle_other 1.297 r_angle_other_deg 1.066 r_mcbond_it 0.919 r_mcbond_other 0.919 r_scbond_it 0.723 r_scbond_other 0.713 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 6564 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing