1VES

Structure of New Antigen Receptor variable domain from sharks


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VER12Y-1 VNAR PDB ENTRY 1VER

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62980.1M Sodium citrate, 20% v/v iso-Propanol, 20% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9458.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.283α = 90
b = 92.046β = 90
c = 98.224γ = 90
Symmetry
Space GroupI 21 21 21

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
12.1818.121000.0540.05432.56.614981
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.182.2499.446.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT12Y-1 VNAR PDB ENTRY 1VER2.1818.121498178399.870.179120.179120.175740.24721RANDOM21.292
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]
-1.070.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.648
r_scangle_it3.05
r_scbond_it1.826
r_angle_refined_deg1.484
r_mcangle_it1.14
r_angle_other_deg0.868
r_mcbond_it0.591
r_nbd_other0.251
r_symmetry_vdw_other0.251
r_symmetry_vdw_refined0.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.648
r_scangle_it3.05
r_scbond_it1.826
r_angle_refined_deg1.484
r_mcangle_it1.14
r_angle_other_deg0.868
r_mcbond_it0.591
r_nbd_other0.251
r_symmetry_vdw_other0.251
r_symmetry_vdw_refined0.208
r_symmetry_hbond_refined0.199
r_nbd_refined0.193
r_xyhbond_nbd_refined0.188
r_chiral_restr0.101
r_nbtor_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1762
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
MOLREPphasing