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The crystal structure of pesticin-T4 lysozyme hybrid stabilized by engineered disulfide bonds
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EPF PDB ENTRIES 4EPF AND 2LZM experimental model PDB 2LZM PDB ENTRIES 4EPF AND 2LZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% w/v PEG3350, 0.25 M calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.86 56.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.397 α = 90 b = 122.882 β = 90 c = 52.299 γ = 90
Symmetry Space Group P 21 21 2
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 300 mm CCD 2009-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.74 45.096 97.9 0.085 21.6 8.3 40579 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.78 94.7 0.577 3 7.8
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 PDB ENTRIES 4EPF AND 2LZM 1.74 45.096 40579 2139 95.37 0.14705 0.14424 0.1404 0.20007 0.1966 RANDOM 23.028
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] 0.85 1.47 -2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.499 r_dihedral_angle_4_deg 14.553 r_dihedral_angle_3_deg 12.266 r_scangle_it 5.427 r_dihedral_angle_1_deg 5.417 r_scbond_it 3.393 r_mcangle_it 2.152 r_rigid_bond_restr 1.716 r_angle_refined_deg 1.338 r_mcbond_it 1.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.499 r_dihedral_angle_4_deg 14.553 r_dihedral_angle_3_deg 12.266 r_scangle_it 5.427 r_dihedral_angle_1_deg 5.417 r_scbond_it 3.393 r_mcangle_it 2.152 r_rigid_bond_restr 1.716 r_angle_refined_deg 1.338 r_mcbond_it 1.253 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2601 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 9
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling