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Crystal structure of Arabidopsis Dehydroquinate dehydratase-shikimate dehydrogenase (T381G mutant) in complex with tartrate and shikimate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 100 mM sodium citrate, pH 4.8, and 2 M ammonium sulfate
20mM quinate
15mg/mL protein
Crystal Properties Matthews coefficient Solvent content 2.86 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.71 α = 90 b = 96.71 β = 90 c = 115.731 γ = 120
Symmetry Space Group P 32 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 RIGAKU SATURN 944+ 2015-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.077 31.66 100 0.03826 0.054 0.038 0.999 13.5 2 38271 28.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.077 2.151 0.3356 0.727 3805
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 FREE R-VALUE 2GPT 2.077 31.656 35865 1772 93.71 0.1997 0.197 0.1968 0.2509 0.2437 Random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.936 f_angle_d 1.083 f_chiral_restr 0.041 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3837 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing