5I1J

CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/IGKV3-11


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M TRIS PH 8.5, 25% PEG 3350, 0.2 M MAGNESIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.5652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.14α = 90
b = 73.83β = 90
c = 102.95γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDRIGAKU SATURN 944VARIMAX HF2009-04-22MSINGLE 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
12.53099.70.0821.1717286-327
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)
12.52.5797.30.2816.96.5

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 SYNTHESISTHROUGHOUT2.5151632887194.60.181320.177340.25764RANDOM38.2
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]
-0.260.20.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.977
r_scbond_it31.869
r_scangle_it28.549
r_dihedral_angle_4_deg17.913
r_dihedral_angle_3_deg15.218
r_dihedral_angle_1_deg6.103
r_mcangle_it4.984
r_mcbond_it2.782
r_angle_refined_deg1.325
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.977
r_scbond_it31.869
r_scangle_it28.549
r_dihedral_angle_4_deg17.913
r_dihedral_angle_3_deg15.218
r_dihedral_angle_1_deg6.103
r_mcangle_it4.984
r_mcbond_it2.782
r_angle_refined_deg1.325
r_chiral_restr0.083
r_bond_refined_d0.009
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 Atoms3248
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms6

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACrefinement
REFMACphasing