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Crystal structure of 3-isopropylmalate dehydrogenase (TM0556) from Thermotoga maritima at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 9 277 25.0% PEG-4000, 0.2M Li2SO4, 0.1M TRIS pH 9.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K 2 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.5 277 20.0% PEG-8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.84 56.62 2.91 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.78 α = 90 b = 118.78 β = 90 c = 56.699 γ = 120
Symmetry Space Group P 3 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 100 CCD ADSC QUANTUM 315 flat mirror 2004-06-27 M SINGLE WAVELENGTH 2 1 x-ray 100 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1 2 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979251, 0.979508, 0.885567 SSRL BL11-1
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 1.9 41.01 99.5 0.11 13.6 5.6 36394 39.46
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 1.9 1.95 97.2 0.684 1.9 3.6 2598
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 MAD THROUGHOUT 1.9 41.01 34079 1801 98.15 0.18934 0.18779 0.1969 0.21822 0.2258 RANDOM 30.46
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] 1.45 0.73 1.45 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.297 r_dihedral_angle_4_deg 19.243 r_dihedral_angle_3_deg 13.779 r_scangle_it 8.908 r_scbond_it 6.495 r_dihedral_angle_1_deg 6.197 r_mcangle_it 3.795 r_mcbond_it 2.902 r_angle_refined_deg 1.673 r_angle_other_deg 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.297 r_dihedral_angle_4_deg 19.243 r_dihedral_angle_3_deg 13.779 r_scangle_it 8.908 r_scbond_it 6.495 r_dihedral_angle_1_deg 6.197 r_mcangle_it 3.795 r_mcbond_it 2.902 r_angle_refined_deg 1.673 r_angle_other_deg 0.872 r_mcbond_other 0.748 r_symmetry_vdw_other 0.219 r_nbd_refined 0.211 r_nbd_other 0.178 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.146 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.109 r_nbtor_other 0.087 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2723 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 1
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SHELX model building autoSHARP phasing SOLOMON phasing REFMAC refinement CCP4 data scaling SHELX phasing