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2.75 Angstrom resolution crystal structure of the A. thaliana LOV2 domain with an extended N-terminal A' helix (cryo dark structure)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V0U PDB ENTRY 2V0U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 287 Protein at 21 mg/mL in 20 mM TRIS-HCl pH 7.4, 20 mM NaCl, 15 % glycerol
Crystallization: The JCSG+ Suite (D12: 0.04 M Potassium phosphate, 16% (w/v) PEG 8000, 20% (v/v) glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.25 45.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.382 α = 90 b = 63.382 β = 90 c = 171.318 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD ADSC QUANTUM 315 Bent conical Si-mirror (Rh coated) 2007-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9002 APS 14-BM-C
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 2.75 30 87.9 0.07 17.5 3.3 8574 8574 -3 66.3
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 2.75 2.8 86.6 0.585 2.2 3.6 399
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2V0U 2.75 29.72 8128 8128 417 88.18 0.23399 0.23109 0.2327 0.2894 0.2909 RANDOM 48.442
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] -1.75 -1.75 3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.087 r_dihedral_angle_3_deg 9.903 r_dihedral_angle_4_deg 7.057 r_dihedral_angle_1_deg 2.771 r_scangle_it 1.787 r_angle_refined_deg 1.312 r_scbond_it 1.071 r_angle_other_deg 0.849 r_mcangle_it 0.8 r_mcbond_it 0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.087 r_dihedral_angle_3_deg 9.903 r_dihedral_angle_4_deg 7.057 r_dihedral_angle_1_deg 2.771 r_scangle_it 1.787 r_angle_refined_deg 1.312 r_scbond_it 1.071 r_angle_other_deg 0.849 r_mcangle_it 0.8 r_mcbond_it 0.421 r_chiral_restr 0.077 r_mcbond_other 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2466 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 63
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling