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Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with 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 7.5 5% PEG-10000, 0.1 M HEPES PH 7.5, MICROSEEDING
Crystal Properties Matthews coefficient Solvent content 2.59 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.49 α = 90 b = 112.01 β = 90 c = 82.26 γ = 90
Symmetry Space Group P 21 21 2
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 EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12
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 98.7 0.12 16.3 6.9 27686 -3 61.5
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 99.5 0.94 2 6.7
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 28.12 26513 982 98.23 0.22782 0.22513 0.2323 0.29764 0.2967 RANDOM 63.916
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] 0.05 -0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.952 r_dihedral_angle_4_deg 14.872 r_dihedral_angle_3_deg 13.511 r_scangle_it 7.996 r_scbond_it 5.048 r_dihedral_angle_1_deg 3.617 r_angle_refined_deg 2.06 r_mcangle_it 1.893 r_mcbond_it 0.974 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.952 r_dihedral_angle_4_deg 14.872 r_dihedral_angle_3_deg 13.511 r_scangle_it 7.996 r_scbond_it 5.048 r_dihedral_angle_1_deg 3.617 r_angle_refined_deg 2.06 r_mcangle_it 1.893 r_mcbond_it 0.974 r_chiral_restr 0.135 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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 5199 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing