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Crystal structure of UPF0235 protein PF1765 from Pyrococcus furiosus crystallized with sodium acetate at pH 8
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 0.2 M Na acetate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.91 35.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.935 α = 90 b = 59.674 β = 90 c = 79.391 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 2025-02-28 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) 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 1.3 39.11 99.9 0.047 0.02 0.999 16.3 6.5 53262 16.917
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 1.3 1.32 98.8 1.026 0.5 0.559 1.4 4.9
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 1.3 39.11 1.34 53190 2646 99.9 0.1872 0.1862 0.1863 0.2051 0.2052 29.54
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 15.154 f_angle_d 1.3676 f_chiral_restr 0.1074 f_plane_restr 0.0194 f_bond_d 0.0139
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1498 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 2
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building