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X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene at5g11950
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293 10 MG/ML PROTEIN, 13% MPEG 2K, 0.28 M POTASSIUM NITRATE, 0.1 M MOPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.589 α = 90 b = 80.427 β = 102.97 c = 50.709 γ = 90
Symmetry Space Group C 1 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 APS-1 SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR 2004-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 2.152 35.451 99.9 0.384 6.266 6.9 25771
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) 2.15 2.23 100 0.384 2.401 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2.152 35.45 25679 1300 99.1 0.16164 0.16164 0.159 0.1843 0.213 0.2302 RANDOM 31.14
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] 0.915 0.386 -0.158 -0.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_4_deg 21.845 r_dihedral_angle_3_deg 14.836 r_scangle_it 6.985 r_dihedral_angle_1_deg 5.547 r_scbond_it 5.121 r_mcangle_it 2.656 r_angle_refined_deg 1.939 r_mcbond_it 1.579 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_4_deg 21.845 r_dihedral_angle_3_deg 14.836 r_scangle_it 6.985 r_dihedral_angle_1_deg 5.547 r_scbond_it 5.121 r_mcangle_it 2.656 r_angle_refined_deg 1.939 r_mcbond_it 1.579 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.271 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.199 r_symmetry_hbond_refined 0.17 r_chiral_restr 0.112 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2798 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement