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Crystal structure of UPF0235 protein PF1765 from Pyrococcus furiosus crystallized with CaCl2 at pH 7
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 7 294 0.2 M Calcium chloride, 0.1 M Hepes pH 7, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.89 35.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.438 α = 90 b = 59.438 β = 90 c = 59.819 γ = 90
Symmetry Space Group P 41 21 2
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 Mirror 2025-04-23 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 42.16 100 0.063 0.064 0.014 0.999 24.1 21.8 19633 20.409
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 1.45 1.48 100 1.407 1.448 0.336 0.771 2.1 18.1
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 42.16 1.34 19527 882 99.7 0.1959 0.1949 0.195 0.2172 0.2173 32.13
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 13.3052 f_angle_d 1.3295 f_chiral_restr 0.1065 f_plane_restr 0.0204 f_bond_d 0.0119
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 761 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building