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Meso-Diaminopimelate Decarboxylase from Arabidopsis thaliana (Isoform 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 277 8 mg/ml protein in buffer containing 0.2 mM PLP and 5 mM lysine mixed in a 1:1 ratio with a reservoir solution consisting of 0.28 M sodium acetate, 0.1 M bis-tris propane pH 7.2, 25%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.381 α = 90 b = 107.989 β = 98.61 c = 80.929 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r 2013-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95369 Australian Synchrotron MX2
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 2.35 39.77 99.7 0.195 0.229 0.118 0.987 5.5 3.7 35978
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 97.9 0.975 1.156 0.615 0.694 3.4
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 2p3e 2.27 46.17 38060 2078 99.36 0.2023 0.1986 0.2025 0.2685 0.2663 RANDOM 29.634
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] -0.11 0.08 0.06 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.719 r_dihedral_angle_4_deg 19.934 r_dihedral_angle_3_deg 16.266 r_dihedral_angle_1_deg 7.887 r_angle_refined_deg 1.556 r_angle_other_deg 1.25 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.719 r_dihedral_angle_4_deg 19.934 r_dihedral_angle_3_deg 16.266 r_dihedral_angle_1_deg 7.887 r_angle_refined_deg 1.556 r_angle_other_deg 1.25 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6424 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing