X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherVk1 O18/O8 germline variable light chain domain monomer

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4295Mother Liquor: 15-30% (w/v) PEG 4K, 0.2 M Li2SO4, 0.1 M TRIS pH 7.9-8.9. Protein: 890 micromolar in 10 mM TRIS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
4.7574.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.054α = 90
b = 176.054β = 90
c = 176.054γ = 90
Symmetry
Space GroupP 41 3 2

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
12.5517699.30.09582.598.7298192981950.3
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)
2.552.64930.479.868.32094

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 REPLACEMENTTHROUGHOUTVk1 O18/O8 germline variable light chain domain monomer2.5535.21298192981952997.730.16620.165470.20601RANDOM18.458
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.93
r_dihedral_angle_3_deg17.465
r_dihedral_angle_4_deg12.731
r_dihedral_angle_1_deg8.026
r_scangle_it3.316
r_scbond_it2.145
r_angle_refined_deg1.832
r_angle_other_deg1.292
r_mcangle_it1.161
r_mcbond_it0.829
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.93
r_dihedral_angle_3_deg17.465
r_dihedral_angle_4_deg12.731
r_dihedral_angle_1_deg8.026
r_scangle_it3.316
r_scbond_it2.145
r_angle_refined_deg1.832
r_angle_other_deg1.292
r_mcangle_it1.161
r_mcbond_it0.829
r_symmetry_vdw_refined0.344
r_symmetry_vdw_other0.235
r_nbd_other0.217
r_nbd_refined0.205
r_xyhbond_nbd_refined0.2
r_nbtor_refined0.188
r_symmetry_hbond_refined0.178
r_mcbond_other0.172
r_chiral_restr0.097
r_nbtor_other0.095
r_xyhbond_nbd_other0.055
r_bond_refined_d0.02
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3490
Nucleic Acid Atoms
Solvent Atoms443
Heterogen Atoms5

Software

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