4XSQ

Structure of a variable lymphocyte receptor-like protein Bf66946 from Branchiostoma floridae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.228915% (w/v) polyethylene glycol 8000, 0.1 M Bis-Tris pH 6.2
Crystal Properties
Matthews coefficientSolvent content
2.3950.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.25α = 90
b = 67.868β = 90
c = 118.041γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97915SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.795095.40.1140.114104.86379537098
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)
11.791.8597.30.4953.64.8

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 DIFFRACTIONSADTHROUGHOUT1.795035225185495.490.179590.178380.20226RANDOM17.726
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]
0.56-0.54-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.804
r_dihedral_angle_3_deg11.31
r_dihedral_angle_4_deg10.68
r_dihedral_angle_1_deg5.889
r_long_range_B_refined4.518
r_long_range_B_other4.517
r_scangle_other2.451
r_scbond_it1.566
r_scbond_other1.566
r_mcangle_it1.474
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.804
r_dihedral_angle_3_deg11.31
r_dihedral_angle_4_deg10.68
r_dihedral_angle_1_deg5.889
r_long_range_B_refined4.518
r_long_range_B_other4.517
r_scangle_other2.451
r_scbond_it1.566
r_scbond_other1.566
r_mcangle_it1.474
r_mcangle_other1.474
r_angle_refined_deg1.252
r_mcbond_it0.915
r_mcbond_other0.915
r_angle_other_deg0.73
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2673
Nucleic Acid Atoms
Solvent Atoms366
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction