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De Novo Three-stranded Coiled Coil Peptide Containing a Tris-thiolate Site Engineered by D-Cysteine Ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Peptide sample: 20 mg/mL peptide, 15 mM Zn(OAc)2 and 5 mM TRIS buffer pH 8.5
Crystallization well condition: 20% (w/v) PEG-8000 and 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.78 67.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.327 α = 90 b = 67.517 β = 90 c = 69.034 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 CCD MARMOSAIC 225 mm CCD 2014-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.69 34.52 99.9 0.076 8.6 7.1 17553 24.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.72 100 0.444 7.2 2748
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 5K92 1.69 34.52 17505 855 99.7 0.18 0.179 0.1832 0.199 0.1999 RANDOM 31.64
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] -1.572 -4.2136 5.7856
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.12 t_omega_torsion 2.26 t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.12 t_omega_torsion 2.26 t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 702 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 16
Software Software Software Name Purpose BUSTER refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing