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SFX Structure of Damage Free Ferric State of Dye Type Peroxidase Aa from Streptomyces lividans
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MAP PDB 5MAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7 291 1:1 ratio of a 6.5 mg/ml DtpAa protein solution with a precipitant solution containing 20% PEG 6000, 100 mM HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.72 α = 90 b = 68.18 β = 105.58 c = 74.62 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 301 CCD MPCCD 2017-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.24 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Silicon nitride fixed target fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Mother liquor
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30 1.66 10.01 (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 1.88 41.46 100 0.993 0.0722 9.6 381 57351
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 1.88 1.91 100 0.722 0.583 1.73 212
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB 5MAP 1.88 35.458 1.35 57312 2852 99.97 0.1336 0.1319 0.147 0.1665 0.1768
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.08 f_angle_d 0.919 f_chiral_restr 0.052 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5466 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling MOLREP phasing