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Crystal structure of UPF0235 protein PF1765 from Pyrococcus furiosus crystallized with sodium citrate 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 1.6 M tri-Na citrate
Crystal Properties Matthews coefficient Solvent content 1.89 34.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.574 α = 90 b = 59.419 β = 90 c = 79.572 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 1.45 47.61 99.2 0.049 0.053 0.02 0.999 20.8 7.2 37840 16.663
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 98.2 1.246 0.49 0.651 1.6 7.3
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 1.45 47.61 1.35 37791 1845 98.98 0.1763 0.1753 0.175 0.1965 0.1962 27.25
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 17.5192 f_angle_d 1.4296 f_chiral_restr 0.1178 f_plane_restr 0.0173 f_bond_d 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1506 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 2
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building