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Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, triclinic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FA3 PDB entry 3FA3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 14% PEG 6000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.09 α = 119.66 b = 115.47 β = 90.71 c = 115.75 γ = 96.28
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 2007-02-27 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 2.18 46.83 93.2 0.086 5.2 2.1 170912 170912
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 2.18 2.26 69.7 0.365 1.7 2 8280
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 3FA3 2.18 46.83 170912 170843 8603 93.2 0.204 0.2 0.2019 0.265 0.2651 RANDOM 36.5
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 -0.18 0.08 -0.18 -0.11 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.985 r_dihedral_angle_4_deg 21.911 r_dihedral_angle_3_deg 19.356 r_dihedral_angle_1_deg 9.867 r_scangle_it 3.352 r_scbond_it 2.311 r_angle_refined_deg 2.088 r_mcangle_it 1.278 r_mcbond_it 0.85 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.985 r_dihedral_angle_4_deg 21.911 r_dihedral_angle_3_deg 19.356 r_dihedral_angle_1_deg 9.867 r_scangle_it 3.352 r_scbond_it 2.311 r_angle_refined_deg 2.088 r_mcangle_it 1.278 r_mcbond_it 0.85 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.245 r_symmetry_hbond_refined 0.239 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.19 r_metal_ion_refined 0.165 r_chiral_restr 0.146 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25258 Nucleic Acid Atoms Solvent Atoms 1162 Heterogen Atoms 12
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling