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Structure of the E270A Mutant Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 20 % PEG 6000, 10 % ethanol, 0.1 M MOPS-K pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 41.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.18 α = 90 b = 143.25 β = 90 c = 174.89 γ = 90
Symmetry Space Group C 2 2 21
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 2012-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.05 99.6 0.072 0.08 17.23 39957 -3 36.093
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 97.9 0.611 0.682 2.71
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2Y41 2.05 30 2009 99.59 0.1731 0.1702 0.1779 0.2288 0.2349 RANDOM 37.048
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] -1.97 3.83 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.96 r_dihedral_angle_4_deg 18.297 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_1_deg 6.046 r_scbond_it 4.783 r_mcangle_it 4.382 r_mcbond_it 3.127 r_angle_refined_deg 1.726 r_chiral_restr 0.11 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.96 r_dihedral_angle_4_deg 18.297 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_1_deg 6.046 r_scbond_it 4.783 r_mcangle_it 4.382 r_mcbond_it 3.127 r_angle_refined_deg 1.726 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5201 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling MOLREP phasing Coot model building PDB_EXTRACT data extraction