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Crystal structure of Arabidopsis thaliana Pdx1K166R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 28.1% PEG 1000 (w/v) and 100 mM HEPES pH 7.
Crystal Properties Matthews coefficient Solvent content 2.81 56.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.001 α = 90 b = 178.001 β = 90 c = 115.127 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2013-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.980023 ESRF ID23-1
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 38.38 98.7 0.112 0.138 0.079 0.987 4.6 2.8 55906
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 2.42 94.4 1.033 1.301 0.779 0.649 2.5
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 FOURIER SYNTHESIS THROUGHOUT 5LNU 2.35 38.38 53102 2796 98.62 0.221 0.2195 0.2577 0.249 0.2808 RANDOM 52.542
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] -4.74 -2.37 -4.74 15.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.189 r_dihedral_angle_4_deg 20.207 r_dihedral_angle_3_deg 14.928 r_dihedral_angle_1_deg 6.423 r_angle_refined_deg 1.516 r_angle_other_deg 1.28 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.189 r_dihedral_angle_4_deg 20.207 r_dihedral_angle_3_deg 14.928 r_dihedral_angle_1_deg 6.423 r_angle_refined_deg 1.516 r_angle_other_deg 1.28 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7870 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction MOLREP phasing