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Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 3 ps Structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 7 295 Combine and vortex 4.45M sodium malonate with 100 uL protein (135 mg/ml initial concentration) for a final sodium malonate concentration of 3.2M. Let stand at room temperature for 1 hour. Spin at 10,000g for 2 hours in small spin concentrators. Vortex and let stand at room temperature for 4 hours. Harvest crystals and rebuffer with 3.0M sodium malonate.
Crystal Properties Matthews coefficient Solvent content 1.88 34.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.9 α = 90 b = 66.9 β = 90 c = 40.8 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 295 PIXEL CS-PAD CXI-1 2015-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.31 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 17.46 98.92 10 1686 13064 13064
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.6 17.46 13064 658 98.92 0.19472 0.19246 0.1832 0.2397 0.2239 RANDOM 6.272
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] -0.04 -0.02 -0.04 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.729 r_dihedral_angle_4_deg 26.796 r_dihedral_angle_3_deg 19.578 r_dihedral_angle_1_deg 7.361 r_long_range_B_refined 3.388 r_long_range_B_other 3.079 r_angle_other_deg 2.567 r_angle_refined_deg 2.408 r_mcangle_it 1.094 r_mcangle_other 1.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.729 r_dihedral_angle_4_deg 26.796 r_dihedral_angle_3_deg 19.578 r_dihedral_angle_1_deg 7.361 r_long_range_B_refined 3.388 r_long_range_B_other 3.079 r_angle_other_deg 2.567 r_angle_refined_deg 2.408 r_mcangle_it 1.094 r_mcangle_other 1.093 r_scangle_other 0.78 r_mcbond_other 0.627 r_mcbond_it 0.626 r_scbond_it 0.463 r_scbond_other 0.463 r_chiral_restr 0.145 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 987 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling