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The Tris-thiolate Zn(II)S3Cl Binding Site Engineered by D-Cysteine Ligands in de Novo Three-stranded Coiled Coil Environment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Peptide sample: 13.2 mg/mL peptide, 15 mM Zn(OAc)2, 5mM TRIS buffer pH 8.5
Crystallization well condition: 40% PEG 400, 0.1M Acetate buffer pH 4.6 (final pH 5.4)
Crystal Properties Matthews coefficient Solvent content 2.11 41.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.119 α = 90 b = 28.977 β = 119.83 c = 43.917 γ = 90
Symmetry Space Group C 1 2 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 CCD MARMOSAIC 225 mm CCD 2008-06-11 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 1.92 26.53 96.7 0.06 15.2 3.5 6290 27.68
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 1.92 1.99 84.9 0.207 2.9 1682
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 3H5F 1.92 26.53 6288 312 96.7 0.198 0.197 0.1992 0.228 0.2335 RANDOM 36.87
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] 1.6166 -10.4653 0.6828 -2.2994
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.16 t_omega_torsion 2.68 t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.16 t_omega_torsion 2.68 t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 670 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 93
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling BUSTER refinement PDB_EXTRACT data extraction MOLREP phasing HKL-2000 data reduction