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Structure of Domain of Unknown Function 507 (DUF507) in Space Group P3(2)21
X-RAY DIFFRACTION - SOLUTION SCATTERING
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8T8K
Solution Scattering Data Acquistion 1 Scattering Type x-ray Radiation/Neutron Source Advanced Light Source Synchrotron Beamline Type 12.3.1 Detector Type Detector Manufacturer Details Pilatus detector Temperature (K) 293 pH Numer of Time Frames Used Protein Concentration Range (mg/mL) Sample Buffer Data Reduction Software Guiner Mean Radius Of Gyration (nm) 22.7 Sigma Mean Radius Of Gyration 0.2 R(XS-1) Mean Cross Sectional Radii (nm) R(XS-1) Sigma Mean Cross Sectional Radii R(XS-2) Mean Cross Sectional Radii (nm) R(XS-2) Sigma Mean Cross Sectional Radii P(R) Protein Length (nm)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286 0.1 M MES monohydrate pH 6.5 and 12% w/v PEG 20,000
Crystal Properties Matthews coefficient Solvent content 3.13 60.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.096 α = 90 b = 83.096 β = 90 c = 68.796 γ = 120
Symmetry Space Group P 32 2 1
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 2022-04-29 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) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.9 41.55 99.8 0.079 0.084 0.026 0.999 18.6 10 21999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 98.5 1.611 1.741 0.643 0.575 6.9
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.9 41.55 0.19 21999 2022 99.78 0.2062 0.2053 0.2074 0.2245 0.2273
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 12.494 f_angle_d 0.634 f_chiral_restr 0.042 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1487 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing