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Crystal structure of UNC119B in complex with LCK peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 30 % w/v PEG 4,000, 0.1 M HEPES pH 7.5, 0.2 M CaCl2
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.083 α = 90 b = 67.004 β = 90 c = 106.691 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 100 PIXEL DECTRIS EIGER X 16M 2019-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91589 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.949 56.742 99.7 0.998 12.7 6.4 29562
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.949 2 0.91
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6H6A 1.949 56.742 29499 1477 99.865 0.184 0.1815 0.1937 0.2239 0.233 32.072
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] -1.963 3.657 -1.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.408 r_dihedral_angle_4_deg 17.012 r_dihedral_angle_3_deg 15.888 r_lrange_it 7.242 r_lrange_other 7.227 r_dihedral_angle_1_deg 7.087 r_scangle_it 5.402 r_scangle_other 5.401 r_mcangle_it 4.067 r_mcangle_other 4.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.408 r_dihedral_angle_4_deg 17.012 r_dihedral_angle_3_deg 15.888 r_lrange_it 7.242 r_lrange_other 7.227 r_dihedral_angle_1_deg 7.087 r_scangle_it 5.402 r_scangle_other 5.401 r_mcangle_it 4.067 r_mcangle_other 4.066 r_scbond_it 3.512 r_scbond_other 3.512 r_mcbond_it 2.734 r_mcbond_other 2.733 r_angle_refined_deg 1.594 r_angle_other_deg 1.29 r_nbd_refined 0.202 r_symmetry_nbd_other 0.202 r_nbd_other 0.199 r_symmetry_nbd_refined 0.178 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.083 r_metal_ion_refined 0.065 r_symmetry_xyhbond_nbd_other 0.058 r_symmetry_metal_ion_refined 0.042 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2862 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing