3MZW

HER2 extracelluar region with affinity matured 3-helix affibody ZHER2:342


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S781S78 and 1LP1
experimental modelPDB 1LP11S78 and 1LP1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52790.05M sodium chloride, 7.5% PEG3350, 0.1M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
3.4564.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.726α = 90
b = 97.841β = 90
c = 148.283γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray115CCDMARMOSAIC 325 mm CCD2008-08-07MSINGLE WAVELENGTH
21x-ray115CCDMARMOSAIC 225 mm CCD2008-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.98SSRLBL11-1
2SYNCHROTRONESRF BEAMLINE ID23-20.87ESRFID23-2

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
1,22.94096.70.09133.92241421673-5-2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1S78 and 1LP12.9402167321673133396.690.208040.203970.27756RANDOM53.182
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]
-1.231.66-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.717
r_dihedral_angle_4_deg20.722
r_dihedral_angle_3_deg19.539
r_dihedral_angle_1_deg6.389
r_scangle_it4.903
r_mcangle_it4.858
r_scbond_it3.117
r_mcbond_it2.985
r_angle_refined_deg1.359
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.717
r_dihedral_angle_4_deg20.722
r_dihedral_angle_3_deg19.539
r_dihedral_angle_1_deg6.389
r_scangle_it4.903
r_mcangle_it4.858
r_scbond_it3.117
r_mcbond_it2.985
r_angle_refined_deg1.359
r_nbtor_refined0.311
r_nbd_refined0.219
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.155
r_chiral_restr0.092
r_symmetry_hbond_refined0.034
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4817
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms56

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling