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Crystal structure of Isocitrate dehydrogenase D252N mutant from Trypanosoma brucei in complexed with NADP+, alpha-ketoglutarate, and ca2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AJA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 14% PEG6000,100MM HEPES BUFFER
Crystal Properties Matthews coefficient Solvent content 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.267 α = 90 b = 89.767 β = 121.04 c = 62.031 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER X 16M 2019-10-25 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) Rrim I (All) CC (Half) 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 1.9 18.94 99.1 0.063 0.07 0.998 14.79 5.3 39065
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.01 98.7 0.496 0.551 0.932 3.61 5.3
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 6AJA 1.9 18.94 37060 1962 99.37 0.20687 0.20528 0.2108 0.23721 0.2416 RANDOM 33.912
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.484 r_dihedral_angle_3_deg 16.865 r_dihedral_angle_4_deg 14.852 r_dihedral_angle_1_deg 5.92 r_long_range_B_refined 4.104 r_long_range_B_other 4.102 r_scangle_other 3.053 r_mcangle_it 2.509 r_mcangle_other 2.509 r_scbond_it 1.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.484 r_dihedral_angle_3_deg 16.865 r_dihedral_angle_4_deg 14.852 r_dihedral_angle_1_deg 5.92 r_long_range_B_refined 4.104 r_long_range_B_other 4.102 r_scangle_other 3.053 r_mcangle_it 2.509 r_mcangle_other 2.509 r_scbond_it 1.914 r_scbond_other 1.911 r_mcbond_it 1.69 r_mcbond_other 1.687 r_angle_refined_deg 1.456 r_angle_other_deg 0.832 r_chiral_restr 0.099 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3191 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing