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Crystal structure of UPF0235 protein PF1765 from Pyrococcus furiosus crystallized with PEG1500 and glycerol at pH 8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9UNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8 294 24% w/v PEG 1500, 20% w/v glycerol
Crystal Properties Matthews coefficient Solvent content 1.91 35.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.079 α = 90 b = 59.703 β = 90 c = 79.266 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 100 CCD MARMOSAIC 225 mm CCD Mirrors 2025-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.978930 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.11 47.69 98 0.04 0.043 0.014 0.999 25.9 9.2 83370 12.852
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.11 1.13 79.1 0.678 0.757 0.33 0.72 2.2 5
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 FREE R-VALUE 9UNT 1.11 26.64 1.34 83276 4164 97.81 0.1883 0.1876 0.1876 0.2022 0.2025 22.28
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 13.5739 f_angle_d 1.2951 f_chiral_restr 0.103 f_plane_restr 0.0196 f_bond_d 0.0129
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1506 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 14
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building