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Crystal structure of the N-terminal domain of CEP164(1-109) bound to camelid nanobody 10Z
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VLV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 292 0.1 M Hepes, pH 7.5, 1.26 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.07 40.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.852 α = 90 b = 70.734 β = 90.09 c = 61.969 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2019-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97942 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 61.97 99.4 0.097 0.04 0.998 9.9 6.7 57658 19.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 98.9 1.463 0.627 0.649 1.7 6.3
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 FREE R-VALUE 5VLV 1.6 61.97 1.34 57454 2843 99.12 0.1819 0.1804 0.1895 0.2108 0.2196 28.06
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 20.0903 f_angle_d 0.7967 f_chiral_restr 0.0507 f_bond_d 0.0058 f_plane_restr 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3396 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing