3L1O

Crystal structure of monoclonal antibody MN423 Fab fragment with free combining site, crystallized in the presence of zinc


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729410% PEG 3350, 0.1M IMIDAZOLE, 0.01M ZNSO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.3748.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.33α = 90
b = 75.426β = 92.86
c = 72.701γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8166EMBL/DESY, HamburgX11

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
1219.984.60.065246842468425.4
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)
122.0599.70.41554.72203

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2V17219.92468423431125381.750.162370.162370.157890.2486RANDOM16.43
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]
2.39-0.17-1.94-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.766
r_dihedral_angle_4_deg21.916
r_dihedral_angle_3_deg15.35
r_dihedral_angle_1_deg7.699
r_scangle_it4.658
r_scbond_it3.182
r_angle_refined_deg2.192
r_mcangle_it1.929
r_mcbond_it1.182
r_angle_other_deg1.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.766
r_dihedral_angle_4_deg21.916
r_dihedral_angle_3_deg15.35
r_dihedral_angle_1_deg7.699
r_scangle_it4.658
r_scbond_it3.182
r_angle_refined_deg2.192
r_mcangle_it1.929
r_mcbond_it1.182
r_angle_other_deg1.109
r_mcbond_other0.387
r_symmetry_vdw_other0.276
r_symmetry_vdw_refined0.22
r_nbd_other0.212
r_nbd_refined0.207
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.156
r_metal_ion_refined0.142
r_chiral_restr0.135
r_nbtor_other0.099
r_bond_refined_d0.027
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_symmetry_metal_ion_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3330
Nucleic Acid Atoms
Solvent Atoms434
Heterogen Atoms8

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling