4LLD

Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain lambda constant domain (IgG1 CH1:Clambda) at 1.19A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3THMpdb entry 3THM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829435% PEG 4K, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
1.8734.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.08α = 90
b = 65.837β = 90
c = 66.925γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77IMAGE PLATEMAR scanner 300 mm plate2012-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1.97949CLSI08ID-1

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
11.1966.92597.60.0436158860110
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)
11.191.2595.60.528

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 3THM1.1946.934615326005630031000.1790.145960.144710.16992RANDOM15.335
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]
0.120.4-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.279
r_dihedral_angle_3_deg11.268
r_dihedral_angle_1_deg6.523
r_scangle_it5.447
r_dihedral_angle_4_deg4.763
r_scbond_it3.867
r_mcangle_it2.924
r_mcbond_it1.828
r_angle_refined_deg1.286
r_rigid_bond_restr1.271
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.279
r_dihedral_angle_3_deg11.268
r_dihedral_angle_1_deg6.523
r_scangle_it5.447
r_dihedral_angle_4_deg4.763
r_scbond_it3.867
r_mcangle_it2.924
r_mcbond_it1.828
r_angle_refined_deg1.286
r_rigid_bond_restr1.271
r_chiral_restr0.078
r_bond_refined_d0.007
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 Atoms1471
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling