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Crystal structure of Trypanosoma cruzi cytosolic isocitrate dehydrogenase in complex with NADP+, isocitrate 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 6.5 293 20% PEG 8000, 100mM imidazole/HCl pH6.5, 3% MPD
Crystal Properties Matthews coefficient Solvent content 2.49 50.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.765 α = 90 b = 123.485 β = 105.96 c = 127.04 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 2017-04-14 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 86.7 0.128 8 3.6 126184
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 88.5 0.734 1.02
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 104805 5493 76.9 0.206 0.202 0.2063 0.283 0.2803 RANDOM 39.14
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] -0.85 -0.91 -1.17 2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.452 r_dihedral_angle_4_deg 19.527 r_dihedral_angle_3_deg 18.369 r_dihedral_angle_1_deg 8.305 r_long_range_B_refined 5.334 r_long_range_B_other 5.334 r_mcangle_it 3.47 r_mcangle_other 3.47 r_scangle_other 3.378 r_mcbond_it 2.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.452 r_dihedral_angle_4_deg 19.527 r_dihedral_angle_3_deg 18.369 r_dihedral_angle_1_deg 8.305 r_long_range_B_refined 5.334 r_long_range_B_other 5.334 r_mcangle_it 3.47 r_mcangle_other 3.47 r_scangle_other 3.378 r_mcbond_it 2.171 r_mcbond_other 2.171 r_scbond_it 2.11 r_scbond_other 2.109 r_angle_refined_deg 1.657 r_angle_other_deg 1.014 r_chiral_restr 0.094 r_bond_refined_d 0.011 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 26288 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 496
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing