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Crystal Structure of domain-swapped C-terminal domain of human doublecortin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IP4 modified PDB entry 5ip4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 293 20 mg/mL protein and 3x cmc CHAPS in 20mM CAPS/NaOH pH10.5, 100mM NaCl, 5mM TCEP mixed 60-70% with 40-30% reservoir consisting of 0.1M HEPES/NaOH pH7.0, 10% PEG 5000 MME, 5% Tacsimate
Crystal Properties Matthews coefficient Solvent content 3.64 66.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.45 α = 90 b = 98.45 β = 90 c = 114.81 γ = 90
Symmetry Space Group P 43 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 PIXEL PSI PILATUS 6M 2014-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.18 44.028 97.5 0.086 0.092 0.999 12.86 8.26 29591 60.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.23 66.5 4.769 5.469 0.27 3.909
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT modified PDB entry 5ip4 2.23 44.028 1.33 28101 1428 99.79 0.2088 0.2075 0.2166 0.2313 0.2449 random 78.9177
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 13.084 f_angle_d 0.922 f_chiral_restr 0.058 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2598 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing