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Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase created by directed evolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X0L PDB ENTRY 1X0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 10% PEG 3350, 27% MPD, 100mM Imidazole (pH 6.5), 200mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.02 59.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.335 α = 90 b = 61.737 β = 98.28 c = 170.054 γ = 90
Symmetry Space Group P 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 95 CCD ADSC QUANTUM 210r 2009-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 50 0.083 0.083 17 67714 67714
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.44 0.346 0.346 2.6
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 1X0L 2.4 49.78 63878 3406 99.19 0.21849 0.21594 0.2205 0.26734 0.27 RANDOM 48.166
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 0.05 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.806 r_dihedral_angle_4_deg 18.84 r_dihedral_angle_3_deg 16.936 r_dihedral_angle_1_deg 5.216 r_scangle_it 1.902 r_scbond_it 1.063 r_angle_refined_deg 1.062 r_mcangle_it 0.771 r_mcbond_it 0.407 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.806 r_dihedral_angle_4_deg 18.84 r_dihedral_angle_3_deg 16.936 r_dihedral_angle_1_deg 5.216 r_scangle_it 1.902 r_scbond_it 1.063 r_angle_refined_deg 1.062 r_mcangle_it 0.771 r_mcbond_it 0.407 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10036 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling