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Structural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Light Structure)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1 M Na acetate pH 4.6, 18-22 % (w/v) PEG-4000, 75-150 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.295 α = 90 b = 91.678 β = 90 c = 34.38 γ = 90
Symmetry Space Group P 21 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 100 CCD ADSC QUANTUM 315 2006-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 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 1.95 15 99.9 0.086 7.8 7.5 21687 21669 2 2
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 1.95 1.98 99.8 0.371 7.6 1050
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 1.95 14.85 21687 21614 1106 99.66 0.184 0.184 0.181 0.1824 0.228 0.234 RANDOM 24.859
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] -0.01 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 15.042 r_dihedral_angle_3_deg 14.444 r_dihedral_angle_1_deg 6.032 r_scangle_it 3.271 r_scbond_it 2.19 r_angle_refined_deg 1.491 r_mcangle_it 1.256 r_mcbond_it 0.854 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 15.042 r_dihedral_angle_3_deg 14.444 r_dihedral_angle_1_deg 6.032 r_scangle_it 3.271 r_scbond_it 2.19 r_angle_refined_deg 1.491 r_mcangle_it 1.256 r_mcbond_it 0.854 r_nbtor_refined 0.306 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2046 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing