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Crystal structure of 14-3-3zeta in complex with a cyclic peptide involving an adamantyl and a dicarboxy side chain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.09 M HEPES sodium salt pH 7.5; 1.26 M tri-Sodium citrate; 10 %(v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 4.6 73.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.92 α = 90 b = 105.74 β = 90 c = 113.93 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 PILATUS3 6M 2015-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.91909 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 2.34 47.77 99.9 0.099 0.108 0.999 12.52 6.52 44013 -3 58.028
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.6 100 0.784 0.852 0.598 2.78
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 (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 3NKX 2.34 47.31 41755 2196 99.91 0.2004 0.1981 0.2161 0.2436 0.2558 RANDOM 55.691
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] 2.64 -0.15 -2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.092 r_dihedral_angle_4_deg 22.723 r_dihedral_angle_3_deg 22.022 r_dihedral_angle_1_deg 6.595 r_angle_refined_deg 2.202 r_angle_other_deg 1.861 r_chiral_restr 0.146 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3709 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing