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Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri in complex with NAD+ and citrate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 21% PEG3350, 0.2M (NH4)2SO4, and 0.1M sodium citrate (pH 5.0)
Crystal Properties Matthews coefficient Solvent content 2.84 56.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.115 α = 90 b = 102.928 β = 104.07 c = 103.29 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 ADSC QUANTUM 315r 2015-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9793 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.87 20 99.4 11.3 5.2 171482
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.97
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.87 20 162895 8559 99.34 0.19663 0.19527 0.2034 0.22222 0.2278 RANDOM 11.922
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] -0.7 -0.56 2.12 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_dihedral_angle_4_deg 18.287 r_dihedral_angle_3_deg 12.603 r_dihedral_angle_1_deg 6.147 r_long_range_B_refined 3.63 r_long_range_B_other 3.63 r_scangle_other 1.553 r_angle_refined_deg 1.477 r_mcangle_it 1.128 r_mcangle_other 1.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_dihedral_angle_4_deg 18.287 r_dihedral_angle_3_deg 12.603 r_dihedral_angle_1_deg 6.147 r_long_range_B_refined 3.63 r_long_range_B_other 3.63 r_scangle_other 1.553 r_angle_refined_deg 1.477 r_mcangle_it 1.128 r_mcangle_other 1.128 r_scbond_it 0.949 r_scbond_other 0.949 r_angle_other_deg 0.945 r_mcbond_it 0.656 r_mcbond_other 0.656 r_chiral_restr 0.109 r_bond_refined_d 0.009 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 12658 Nucleic Acid Atoms Solvent Atoms 1216 Heterogen Atoms 305
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing