2COQ

Structure of new antigen receptor variable domain from sharks


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VERPDB ENTRY 1VER

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.52980.1M Chess PH9.5, 50% PEG200, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.141.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.268α = 90
b = 68.324β = 90
c = 39.511γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315RH COATED SI MIRROR2004-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.134.298.550.12615.27.2633635.3
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)
12.12.151000.9772

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VER2.134.26336633628998.550.220420.220420.217530.28048RANDOM49.94
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]
-2.32.140.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.342
r_dihedral_angle_3_deg17.825
r_dihedral_angle_4_deg13.958
r_dihedral_angle_1_deg7.26
r_scangle_it2.443
r_scbond_it1.564
r_angle_refined_deg1.494
r_mcangle_it0.911
r_mcbond_it0.527
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.342
r_dihedral_angle_3_deg17.825
r_dihedral_angle_4_deg13.958
r_dihedral_angle_1_deg7.26
r_scangle_it2.443
r_scbond_it1.564
r_angle_refined_deg1.494
r_mcangle_it0.911
r_mcbond_it0.527
r_nbtor_refined0.307
r_nbd_refined0.266
r_symmetry_hbond_refined0.246
r_xyhbond_nbd_refined0.232
r_symmetry_vdw_refined0.21
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms823
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
MOLREPphasing