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Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with NADH and Mn
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y3Z PDB ENTRY 2Y3Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 15% PEG-20000, 2% DIOXANE, 0.1 M BICINE PH 9.0
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.38 α = 90 b = 161.45 β = 91.96 c = 83.91 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 MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.5 99 99.9 0.13 10.8 4.2 51742 -3 44
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 2.5 2.56 99 0.57 2.1 3.8
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 PDB ENTRY 2Y3Z 2.5 19.72 49505 2109 99.91 0.17951 0.17637 0.1851 0.25422 0.2538 RANDOM 49.541
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] 0.04 0.02 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.953 r_dihedral_angle_4_deg 20.486 r_dihedral_angle_3_deg 16.65 r_scangle_it 7.237 r_dihedral_angle_1_deg 5.82 r_scbond_it 4.326 r_angle_refined_deg 1.563 r_mcangle_it 1.385 r_mcbond_it 0.673 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.953 r_dihedral_angle_4_deg 20.486 r_dihedral_angle_3_deg 16.65 r_scangle_it 7.237 r_dihedral_angle_1_deg 5.82 r_scbond_it 4.326 r_angle_refined_deg 1.563 r_mcangle_it 1.385 r_mcbond_it 0.673 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10542 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 235
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing