3C09

Crystal structure the Fab fragment of matuzumab (Fab72000) in complex with domain III of the extracellular region of EGFR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YY91YY9, 3C08
experimental modelPDB 3C081YY9, 3C08

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION629816% PEG 3350, 1M NaCl, pH 6.0, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.6866.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.073α = 90
b = 205.035β = 117.49
c = 81.577γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mmMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.25099.70.1188.33.53388633886
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.3198.70.3543.23339

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 REPLACEMENTTHROUGHOUT1YY9, 3C083.236.563373832028170899.730.2450.2420.299RANDOM47.909
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]
0.790.21-0.38-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.604
r_dihedral_angle_3_deg19.885
r_dihedral_angle_4_deg16.97
r_dihedral_angle_1_deg7.04
r_angle_refined_deg1.333
r_scangle_it1.229
r_mcangle_it0.797
r_scbond_it0.729
r_mcbond_it0.432
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.604
r_dihedral_angle_3_deg19.885
r_dihedral_angle_4_deg16.97
r_dihedral_angle_1_deg7.04
r_angle_refined_deg1.333
r_scangle_it1.229
r_mcangle_it0.797
r_scbond_it0.729
r_mcbond_it0.432
r_nbtor_refined0.316
r_symmetry_vdw_refined0.303
r_nbd_refined0.255
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.124
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms8359
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms173

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction