2Q20

Structure of the germline Vk1 O18/O8 light chain variable domain homodimer


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BREpolyserine model of pdb entry 1BRE chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295Protein: 890 micromolar in 10 mM TRIS pH 7.4. Mother Liquor: 15-30% (w/v) PEG 4K, 0.2 Li2SO4, 0.1 M TRIS pH 7.9-8.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.2962.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.265α = 90
b = 74.265β = 90
c = 99.051γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3mirror2007-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM1.0718APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.39999.70.04653.212.2748397483922.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.31.3396.30.532.35.65311

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpolyserine model of pdb entry 1BRE chain A1.399748397483953599.190.119550.119350.14815RANDOM14.491
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]
0.060.030.06-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.932
r_dihedral_angle_4_deg19.808
r_sphericity_free16.821
r_dihedral_angle_3_deg11.163
r_dihedral_angle_1_deg6.402
r_scangle_it5.511
r_scbond_it4.5
r_sphericity_bonded4.388
r_mcangle_it2.977
r_mcbond_it2.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.932
r_dihedral_angle_4_deg19.808
r_sphericity_free16.821
r_dihedral_angle_3_deg11.163
r_dihedral_angle_1_deg6.402
r_scangle_it5.511
r_scbond_it4.5
r_sphericity_bonded4.388
r_mcangle_it2.977
r_mcbond_it2.459
r_rigid_bond_restr2.333
r_angle_other_deg2.164
r_angle_refined_deg1.773
r_mcbond_other1.682
r_xyhbond_nbd_refined0.301
r_nbd_refined0.265
r_symmetry_vdw_other0.232
r_nbd_other0.225
r_symmetry_hbond_refined0.224
r_nbtor_refined0.193
r_symmetry_vdw_refined0.132
r_chiral_restr0.117
r_nbtor_other0.091
r_xyhbond_nbd_other0.062
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_gen_planes_other0.007
r_bond_other_d0.003
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1970
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing