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Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane pH 7.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.57 α = 90 b = 160.57 β = 90 c = 161.41 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2007-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.6 50 94.3 0.135 5.1 2.4 135034 135034
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 2.6 2.69 90.2 0.414 1.9 2.2 9535
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.6 50 135034 135026 6752 94.3 0.193 0.19 0.1901 0.255 0.2524 RANDOM 37.6
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] -0.16 -0.08 -0.16 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.109 r_dihedral_angle_4_deg 21.627 r_dihedral_angle_3_deg 21.25 r_dihedral_angle_1_deg 14.728 r_scangle_it 2.343 r_angle_refined_deg 2.145 r_scbond_it 1.631 r_mcangle_it 0.872 r_mcbond_it 0.653 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.109 r_dihedral_angle_4_deg 21.627 r_dihedral_angle_3_deg 21.25 r_dihedral_angle_1_deg 14.728 r_scangle_it 2.343 r_angle_refined_deg 2.145 r_scbond_it 1.631 r_mcangle_it 0.872 r_mcbond_it 0.653 r_nbtor_refined 0.322 r_symmetry_hbond_refined 0.267 r_nbd_refined 0.256 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.137 r_bond_refined_d 0.022 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 35442 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 214
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling