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SFX structure of dye-type peroxidase DtpB D152A variant in the ferric state
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 291 6.2 mg/mL of protein in 20mM Sodium phosphate, 150mM NaCl pH 7 mixed with 1250 mM MgCl2, 125 mM HEPES, 18% PEG 4000, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.5 α = 90 b = 121.1 β = 90 c = 198 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 2021-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.127 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 high-viscosity cartridge-type (HVC) injector injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) undefined (KeV)
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 0.0068 (µl/min) undefined (µm) Gas hydroxyethyl cellulose matrix
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 1.92 36.01 100 0.979 0.125 7.14 606 158842
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 1.92 1.94 100 0.452 0.887 427
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 6YRJ 1.92 36.01 150815 8027 99.98 0.1744 0.1729 0.1825 0.202 0.2089 RANDOM 30.768
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 -0.06 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.249 r_dihedral_angle_2_deg 12.757 r_dihedral_angle_1_deg 6.64 r_angle_refined_deg 1.767 r_angle_other_deg 0.611 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13901 Nucleic Acid Atoms Solvent Atoms 772 Heterogen Atoms 260
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling REFMAC phasing