2I24 | pdb_00002i24

Crystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SQ2PDB ENTRY 1SQ2, CHAIN N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.427724% PEG 400, 0.1M Na/K phosphate, 0.15M NaCl, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.958α = 90
b = 53.958β = 90
c = 79.077γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-01-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.97623ALS8.2.1

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
11.3544.798.70.05616.73.82606026060-314
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)
1.351.3795.60.461.91.951226

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1SQ2, CHAIN N1.3544.72475324753125398.710.17410.172120.240.21430.26RANDOM17.858
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]
-0.37-0.370.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.123
r_dihedral_angle_4_deg16.629
r_dihedral_angle_3_deg9.976
r_sphericity_free9.864
r_dihedral_angle_1_deg6.18
r_scangle_it5.339
r_scbond_it4.469
r_sphericity_bonded4.061
r_mcangle_it3.02
r_mcbond_it2.569
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms872
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
EPMRphasing