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Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 20% PEG 3350, 200mM potassium nitrate
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.442 α = 90 b = 109.754 β = 89.98 c = 64.961 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 2015-12-12 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 3.2 50 98.4 0.099 6.6 3.3 14385
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 3.2 3.26 99.2 0.799 1.45 3.2
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 1T0L 3.2 45.02 11582 558 83.88 0.21649 0.21219 0.2282 0.30858 0.3126 RANDOM 79.105
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] 20.92 26.33 -17.14 -3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.716 r_dihedral_angle_3_deg 22.999 r_dihedral_angle_4_deg 16.827 r_long_range_B_refined 11.723 r_long_range_B_other 11.722 r_dihedral_angle_1_deg 10.41 r_mcangle_it 7.735 r_mcangle_other 7.734 r_scangle_other 6.317 r_mcbond_it 4.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.716 r_dihedral_angle_3_deg 22.999 r_dihedral_angle_4_deg 16.827 r_long_range_B_refined 11.723 r_long_range_B_other 11.722 r_dihedral_angle_1_deg 10.41 r_mcangle_it 7.735 r_mcangle_other 7.734 r_scangle_other 6.317 r_mcbond_it 4.593 r_mcbond_other 4.592 r_scbond_it 3.682 r_scbond_other 3.682 r_angle_refined_deg 1.875 r_angle_other_deg 1.138 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing