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Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: Dark structure of photoactive yellow protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 7 295 4.45M Sodium malonate (pH7) injected into concentrated protein for a final malonate concentration of 3.2M. Sit for 1 hour at room temperature. Spin in spin concentrator for 2 hours. Sit at room temperature for 4 hours. Crystals are harvested and resuspended in 3.0M 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 98.39 10 992 13060 13060
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 13060 685 98.39 0.15492 0.15355 0.1551 0.18119 0.1855 RANDOM 14.796
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 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.881 r_dihedral_angle_3_deg 17.153 r_dihedral_angle_4_deg 10.079 r_dihedral_angle_1_deg 7.087 r_long_range_B_refined 6.483 r_long_range_B_other 6.221 r_scangle_other 4.805 r_scbond_it 3.046 r_scbond_other 3.046 r_mcangle_it 2.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.881 r_dihedral_angle_3_deg 17.153 r_dihedral_angle_4_deg 10.079 r_dihedral_angle_1_deg 7.087 r_long_range_B_refined 6.483 r_long_range_B_other 6.221 r_scangle_other 4.805 r_scbond_it 3.046 r_scbond_other 3.046 r_mcangle_it 2.528 r_mcangle_other 2.528 r_angle_refined_deg 2.046 r_mcbond_it 1.612 r_mcbond_other 1.61 r_angle_other_deg 1.064 r_chiral_restr 0.165 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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