5I1E

CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-53/IGKV1-39


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29316% PEG 3K, 0.2 M AMMONIUM SULFATE, 5% DIOXANE
Crystal Properties
Matthews coefficientSolvent content
2.5752

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.38α = 90
b = 89.38β = 90
c = 212.38γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDRIGAKU SATURN 944VARIMAX HF2009-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.73099.60.09538.320.614402-333.2
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)
12.72.7796.80.4518.119.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.7151358372294.60.194550.190890.26362RANDOM49.1
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]
0.370.190.37-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it40.751
r_scangle_it40.34
r_dihedral_angle_2_deg35.847
r_dihedral_angle_4_deg19.178
r_dihedral_angle_3_deg16.616
r_dihedral_angle_1_deg6.346
r_mcangle_it4.735
r_mcbond_it2.307
r_angle_refined_deg1.213
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it40.751
r_scangle_it40.34
r_dihedral_angle_2_deg35.847
r_dihedral_angle_4_deg19.178
r_dihedral_angle_3_deg16.616
r_dihedral_angle_1_deg6.346
r_mcangle_it4.735
r_mcbond_it2.307
r_angle_refined_deg1.213
r_chiral_restr0.073
r_bond_refined_d0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3236
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms11

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACrefinement
REFMACphasing