5I19

CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-23/IGKV1-39


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I1D5I1D,4KMT
experimental modelPDB 4KMT5I1D,4KMT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% PEG 3350, 0.2 M LITHIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.56α = 90
b = 96.56β = 90
c = 105.39γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDRIGAKU SATURN 944VARIMAX HF2009-05-06MSINGLE 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
12.83099.50.09131.21412678-342.8
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)
12.82.8897.40.5945.113.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5I1D,4KMT2.8151197261294.60.242930.239430.31544RANDOM48.4
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]
1.191.19-2.39
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it42.343
r_scbond_it39.954
r_dihedral_angle_2_deg34.162
r_dihedral_angle_4_deg22.233
r_dihedral_angle_3_deg17.198
r_dihedral_angle_1_deg5.949
r_mcangle_it4.03
r_mcbond_it1.917
r_angle_refined_deg1.262
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it42.343
r_scbond_it39.954
r_dihedral_angle_2_deg34.162
r_dihedral_angle_4_deg22.233
r_dihedral_angle_3_deg17.198
r_dihedral_angle_1_deg5.949
r_mcangle_it4.03
r_mcbond_it1.917
r_angle_refined_deg1.262
r_chiral_restr0.076
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 Atoms3234
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement