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X-Ray Structure of a Lysine Decarboxylase-Like Protein from Arabidopsis Thaliana Gene AT2G37210
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDH PDB ENTRY 1YDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 296 10 MG/ML PROTEIN, 22% PEG 2K, 0.084 M MAGNESIUM SULFATE,
0.100 M BISTRIS, vapor diffusion, hanging drop, temperature 296K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 1.9 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.403 α = 90 b = 66.773 β = 90 c = 98.639 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-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 1.95 50 99.8 0.1 15.009 10.7 26424
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) 1.95 2.02 98.6 0.518 1.756 4.8
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 PDB ENTRY 1YDH 1.95 46.984 25025 1336 99.8 0.183 0.181 0.192 0.234 0.2384 RANDOM 29.22
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] -0.34 -0.31 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_dihedral_angle_4_deg 19.02 r_dihedral_angle_3_deg 15.764 r_scangle_it 7.146 r_dihedral_angle_1_deg 6.324 r_scbond_it 5.342 r_mcangle_it 2.946 r_mcbond_it 1.861 r_angle_refined_deg 1.712 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_dihedral_angle_4_deg 19.02 r_dihedral_angle_3_deg 15.764 r_scangle_it 7.146 r_dihedral_angle_1_deg 6.324 r_scbond_it 5.342 r_mcangle_it 2.946 r_mcbond_it 1.861 r_angle_refined_deg 1.712 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.271 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.135 r_symmetry_hbond_refined 0.126 r_metal_ion_refined 0.026 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 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_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 2636 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction