3GKW

Crystal structure of the Fab fragment of Nimotuzumab. An anti-epidermal growth factor receptor antibody


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.752930.1 M MES, 25% PEG 1000, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5652.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.223α = 90
b = 84.223β = 90
c = 138.535γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirror2003-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7110.97MAX III711

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
12.520980.12516.77175561748611
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)
12.52.56980.4893.66.8

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 REPLACEMENTTHROUGHOUTPDB entry 1uyw2.519.79175561667888998.010.217470.213790.28375RANDOM15.43
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]
-0.33-0.330.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.558
r_dihedral_angle_4_deg21.64
r_dihedral_angle_3_deg18.698
r_dihedral_angle_1_deg6.978
r_scangle_it3.343
r_scbond_it2.167
r_angle_refined_deg1.701
r_mcangle_it1.37
r_mcbond_it0.704
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.558
r_dihedral_angle_4_deg21.64
r_dihedral_angle_3_deg18.698
r_dihedral_angle_1_deg6.978
r_scangle_it3.343
r_scbond_it2.167
r_angle_refined_deg1.701
r_mcangle_it1.37
r_mcbond_it0.704
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3078
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms23

Software

Software
Software NamePurpose
BLi711data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling