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SFX structure of dye-type peroxidase DtpB in the ferryl state
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other unpublished structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 293 6-10 mg/mL of protein in 50mM Sodium acetate, 150mM NaCl pH 5 was mixed with 150 mM MgCl2, 150 mM HEPES, 20% PEG 4000 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.51 50.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.3 α = 90 b = 120 β = 90 c = 198.45 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 301 CCD MPCCD 2019-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.13 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 silicon chip fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 silicon chip 25600 apertures per chip
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 11 (KeV)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.75 102 100 0.984 0.109 6.1 1943 207440 28.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 0.423 0.887
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT unpublished structure 1.75 13 196370 10353 99.67 0.1682 0.1666 0.1764 0.1988 0.2067 RANDOM 33.628
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 -0.36 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.319 r_dihedral_angle_4_deg 17.361 r_dihedral_angle_3_deg 13.019 r_dihedral_angle_1_deg 6.771 r_angle_refined_deg 1.626 r_angle_other_deg 1.445 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.319 r_dihedral_angle_4_deg 17.361 r_dihedral_angle_3_deg 13.019 r_dihedral_angle_1_deg 6.771 r_angle_refined_deg 1.626 r_angle_other_deg 1.445 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13904 Nucleic Acid Atoms Solvent Atoms 880 Heterogen Atoms 279
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling REFMAC phasing