1VER

Structure of New Antigen Receptor variable domain from sharks


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M BIS-TRIS PROPANE, 45% PPG P400, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1460.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.259α = 90
b = 97.259β = 90
c = 65.228γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATEMAR scanner 180 mm plateAxco microcapillary focusing optics2003-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.8269.01990.0450.04518.115.13975
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.822.994.31.84.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUT2.826335315399.290.169720.169720.165880.25391RANDOM40.21
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]
3.533.53-7.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.873
r_scangle_it1.864
r_angle_refined_deg1.552
r_scbond_it1.038
r_angle_other_deg0.838
r_mcangle_it0.69
r_symmetry_vdw_refined0.37
r_symmetry_vdw_other0.364
r_mcbond_it0.363
r_nbd_other0.224
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.873
r_scangle_it1.864
r_angle_refined_deg1.552
r_scbond_it1.038
r_angle_other_deg0.838
r_mcangle_it0.69
r_symmetry_vdw_refined0.37
r_symmetry_vdw_other0.364
r_mcbond_it0.363
r_nbd_other0.224
r_nbd_refined0.22
r_xyhbond_nbd_refined0.22
r_symmetry_hbond_refined0.16
r_nbtor_other0.089
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms770
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement