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Crystal structure of UPF0235 protein PF1765 from Pyrococcus furiosus crystallized with CaCl2 at pH 6
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 6 294 0.2 M Calcium chloride, 0.1 M MES pH 6, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.81 32.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.99 α = 90 b = 58.99 β = 90 c = 58.061 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 Mirrors 2025-04-20 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 1.5 41.71 100 0.042 0.049 0.01 1 31.6 22.5 17025 24.197
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 1.5 1.53 100 1.553 1.588 0.33 0.85 2.2 23
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 1.5 33.88 1.33 16723 748 98.47 0.2126 0.2116 0.2114 0.2361 0.2359 35.27
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 19.223 f_angle_d 1.33 f_chiral_restr 0.0886 f_plane_restr 0.0186 f_bond_d 0.0133
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 744 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 2
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building