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Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 100 fs to 400 fs 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 19.31 98.72 10 300 13039 13039
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 19.31 13039 655 98.72 0.21068 0.2083 0.2004 0.25832 0.247 RANDOM 5.462
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 -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.61 r_dihedral_angle_4_deg 24.443 r_dihedral_angle_3_deg 21.6 r_dihedral_angle_1_deg 8.04 r_long_range_B_refined 2.993 r_long_range_B_other 2.651 r_angle_other_deg 2.557 r_angle_refined_deg 2.372 r_mcangle_it 0.713 r_mcangle_other 0.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.61 r_dihedral_angle_4_deg 24.443 r_dihedral_angle_3_deg 21.6 r_dihedral_angle_1_deg 8.04 r_long_range_B_refined 2.993 r_long_range_B_other 2.651 r_angle_other_deg 2.557 r_angle_refined_deg 2.372 r_mcangle_it 0.713 r_mcangle_other 0.712 r_scangle_other 0.509 r_mcbond_it 0.413 r_mcbond_other 0.413 r_scbond_it 0.313 r_scbond_other 0.313 r_chiral_restr 0.132 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 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