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Room temperature structure of Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate and Factor X derived peptide fragment
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q9F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 278 16% PEG 3350, 0.1 M Bis Tris propane pH 7.5, 0.1 M KSCN
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.796 α = 90 b = 88.16 β = 90 c = 125.161 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 293 CCD RAYONIX MX340-HS 2023-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.50844 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 ADE tape drive injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) 30 1.8 (KeV)
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 ADE tape drive 7 (µl/min) undefined (µm)
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 1.95 26.64 99.86 0.98 0.152 3.342 40.35 41728 36.01
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 1.95 1.98 98.86 0.165 1.094 0.412 10.96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.95 26.64 1.34 41564 2000 99.52 0.1785 0.1771 0.1778 0.2066 0.2058 44.95
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 13.8234 f_angle_d 0.8593 f_chiral_restr 0.0503 f_plane_restr 0.0074 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3498 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement cctbx.xfel data reduction cctbx.xfel.merge data scaling PHASER phasing