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Structure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AG-I promoter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VY1 PDB ENTRY 2VY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 10% PEG 400, 100 MM KCL, 10 MM CACL2, 50 MM HEPES (NAOH) PH 7.0
Crystal Properties Matthews coefficient Solvent content 5.21 78.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.85 α = 90 b = 98.85 β = 90 c = 177.4 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 210 2007-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.3 20 99.8 0.08 26.7 14 328932 3 38.53
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 2.3 2.4 100 0.75 3.4 11.4
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2VY1 2.3 19.951 2.05 23413 1183 99.85 0.2315 0.23 0.218 0.2619 0.2508 46.22
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] -1.6689 -1.6689 -6.537
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.327 f_angle_d 1.394 f_chiral_restr 0.071 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1326 Nucleic Acid Atoms 565 Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling REFMAC phasing