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PDZ domain from choanoflagellate GIPC (mbGIPC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V6B PDB entry 5V6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1 M ammonium tartrate dibasic, pH 7.0, 12% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.709 α = 90 b = 35.301 β = 90 c = 82.773 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 2019-05-10 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 1.198 41.386 91.4 0.914 1 31.9 5.34 28166 12.3
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 1.2 1.27 52.9 0.115 0.973 5.15 1.63
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 5V6B 1.198 41.386 1.37 27011 1335 95.84 0.1678 0.1666 0.168 0.189 0.1901 12.373
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 15.313 f_angle_d 0.818 f_chiral_restr 0.086 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 707 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 6
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing