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DtpAa Y389F 53 fs 100 microjoules XFEL Pulse Data Collection
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 298 12% v/v PEG 3350, 100 mM HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.72 α = 90 b = 68.2 β = 105.6 c = 74.6 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 294.15 PIXEL PSI JUNGFRAU 8M 2023-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SwissFEL ARAMIS BEAMLINE ESA 1.03 SwissFEL ARAMIS ESA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.31 35.05 100 0.914 4.13 187.6 172313
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.31 1.34 100 0.486 1.27 118.3
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 MOLECULAR REPLACEMENT THROUGHOUT 1.33 35.05 152910 7961 99.98 0.15403 0.15325 0.1956 0.16937 0.1949 RANDOM 18.339
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] 0.23 -0.03 -0.32 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.628 r_dihedral_angle_2_deg 10.484 r_dihedral_angle_1_deg 6.302 r_long_range_B_refined 5.952 r_long_range_B_other 5.909 r_scangle_other 4.946 r_scbond_other 3.208 r_scbond_it 3.207 r_mcangle_other 2.492 r_mcangle_it 2.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.628 r_dihedral_angle_2_deg 10.484 r_dihedral_angle_1_deg 6.302 r_long_range_B_refined 5.952 r_long_range_B_other 5.909 r_scangle_other 4.946 r_scbond_other 3.208 r_scbond_it 3.207 r_mcangle_other 2.492 r_mcangle_it 2.489 r_angle_refined_deg 1.88 r_mcbond_it 1.708 r_mcbond_other 1.705 r_angle_other_deg 0.644 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 5548 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement CrystFEL data scaling CrystFEL data reduction Coot model building PHASER phasing