4EPI

The crystal structure of pesticin-T4 lysozyme hybrid stabilized by engineered disulfide bonds


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EPFPDB ENTRIES 4EPF AND 2LZM
experimental modelPDB 2LZMPDB ENTRIES 4EPF AND 2LZM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529820% w/v PEG3350, 0.25 M calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8656.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.397α = 90
b = 122.882β = 90
c = 52.299γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7445.09697.90.08521.68.34057911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.7894.70.57737.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 4EPF AND 2LZM1.7445.09640579213995.370.147050.144240.20007RANDOM23.028
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]
0.851.47-2.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.499
r_dihedral_angle_4_deg14.553
r_dihedral_angle_3_deg12.266
r_scangle_it5.427
r_dihedral_angle_1_deg5.417
r_scbond_it3.393
r_mcangle_it2.152
r_rigid_bond_restr1.716
r_angle_refined_deg1.338
r_mcbond_it1.253
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.499
r_dihedral_angle_4_deg14.553
r_dihedral_angle_3_deg12.266
r_scangle_it5.427
r_dihedral_angle_1_deg5.417
r_scbond_it3.393
r_mcangle_it2.152
r_rigid_bond_restr1.716
r_angle_refined_deg1.338
r_mcbond_it1.253
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.006
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 AtomsNumber
Protein Atoms2601
Nucleic Acid Atoms
Solvent Atoms561
Heterogen Atoms9

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling