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Structure of Domain of Unknown Function 507 (DUF507) in Space Group C222(1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold O67633
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 286 0.01 M Co(II)Cl2 hexahydrate, 0.1 M sodium acetate pH 4.6, and 1.0 M 1,6-hexanediol
Crystal Properties Matthews coefficient Solvent content 2.84 56.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.714 α = 90 b = 86.534 β = 90 c = 79.139 γ = 90
Symmetry Space Group C 2 2 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 CMOS RDI CMOS_8M 2022-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0722 ALS 4.2.2
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 1.87 45.53 99.8 0.081 0.088 0.034 0.998 14.9 6.9 20928
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 1.87 1.91 99 0.618 0.668 0.253 0.879 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.88 45.53 1.35 20563 987 98.87 0.2187 0.2171 0.2166 0.2528 0.2509
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 11.843 f_angle_d 0.468 f_chiral_restr 0.037 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1510 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing