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Meso-Diaminopimelate Decarboxylase from Arabidopsis thaliana (Isoform 1)
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 7.5 277 8 mg/ml protein in buffer containing 0.2 mM PLP and 0.4 mM lysine mixed in a 1:1 ratio with a reservoir solution consisting of 0.2 M magnesium chloride, 0.1 M Tris pH 7.5, 20%(w/v) PEG 6000.
Crystal Properties Matthews coefficient Solvent content 2.22 47.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.968 α = 90 b = 88.624 β = 90 c = 121.587 γ = 90
Symmetry Space Group P 21 2 21
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 1.88 42.62 99.9 0.147 0.158 0.058 0.997 9.6 7.3 71841
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 1.88 1.92 98.7 1.301 1.407 0.531 0.678 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2p3e 1.88 42.66 69528 2260 99.9 0.1717 0.1703 0.2142 0.2032 RANDOM 24.775
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] -0.05 0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.602 r_dihedral_angle_4_deg 17.428 r_dihedral_angle_3_deg 14.64 r_dihedral_angle_1_deg 7.499 r_angle_refined_deg 1.573 r_angle_other_deg 1.384 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.602 r_dihedral_angle_4_deg 17.428 r_dihedral_angle_3_deg 14.64 r_dihedral_angle_1_deg 7.499 r_angle_refined_deg 1.573 r_angle_other_deg 1.384 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6451 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing