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Dehaloperoxidase B from Amphitrite ornata - complex with 2,4-dichlorophenol
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6 277 5.5 mg/ml DHP-B in 20 mM MES pH 6.0 mixed with 35% PEG 4000, 200 mM AmSO4 at a ratio of 1:4 in a total volume of 250 microlitres
Crystal Properties Matthews coefficient Solvent content 2.28 46.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.94 α = 90 b = 67.15 β = 90 c = 68.72 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 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 1.85 37.7 100 0.99 0.066 10.4 579 24749
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 1.85 1.9 100 0.66 1.64 340
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 3ixf 1.85 34.36 1.34 24690 1255 99.97 0.1693 0.1676 0.1818 0.1991 0.2088 42.4806
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2102 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 113
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling MOLREP phasing