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Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ2 (mbDLG-2) in spacegroup P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BYG PDB entry 2BYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 0.2 M sodium malonate, pH 5, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.091 α = 90 b = 56.107 β = 90 c = 57.918 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 80 PIXEL DECTRIS PILATUS3 6M 2020-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977410 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 40.3 99.4 0.033 1 24.04 6.04 28809 24.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.38 96.5 0.36 0.866 2.48 3.61
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 THROUGHOUT PDB entry 2BYG 1.3 40.299 1.35 28680 1432 99.61 0.1956 0.195 0.2008 0.2072 0.2134 24.4252
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 25.536 f_angle_d 0.769 f_chiral_restr 0.083 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 697 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 6
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing