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Time Resolved Serial Femtosecond Crystallography Captures High Resolution Intermediates of PYP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7 296 Microcrystals of ~2 x 2 x 5 um3 size were created by centrifugation in spin filters
Crystal Properties Matthews coefficient Solvent content 1.9 35.19
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 100 PIXEL CS-PAD detector 2014-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.36 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Split (All) 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 16.73 100 0.092 8.7 1500 13500
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 2PHY 1.6 16.73 13161 694 99.89 0.22194 0.2188 0.219 0.28272 0.283 RANDOM 25.831
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] -0.14 -0.07 -0.14 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.37 r_dihedral_angle_3_deg 19.374 r_dihedral_angle_4_deg 19.01 r_long_range_B_refined 6.924 r_dihedral_angle_1_deg 6.202 r_scbond_it 3.222 r_mcangle_it 3.177 r_mcbond_it 2.387 r_angle_refined_deg 2.325 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.37 r_dihedral_angle_3_deg 19.374 r_dihedral_angle_4_deg 19.01 r_long_range_B_refined 6.924 r_dihedral_angle_1_deg 6.202 r_scbond_it 3.222 r_mcangle_it 3.177 r_mcbond_it 2.387 r_angle_refined_deg 2.325 r_chiral_restr 0.147 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 976 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement