4NOF

Crystal structure of the second Ig domain from mouse Polymeric Immunoglobulin receptor [PSI-NYSGRC-006220]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XEDPoly-alanine model of PDB code 1XED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3.5298Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 5% glycerol), Reservoir (0.1 M Citric Acid:NaOH pH 3.5, 25% (w/v) PEG 3350), Cryoprotection (30% Glycerol), Vapor Diffusion, Sitting Drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.388α = 90
b = 35.365β = 105.96
c = 73.238γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2013-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0750NSLSX29A

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
11.655098.60.08218.36301813018121.9
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)
11.651.68940.7021.8951467

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPoly-alanine model of PDB code 1XED1.655030082152298.620.1810.180.1992RANDOM27.9053
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]
0.84-0.771.15-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.297
r_dihedral_angle_4_deg21.406
r_dihedral_angle_3_deg11.739
r_dihedral_angle_1_deg6.358
r_mcangle_it3.486
r_mcbond_it2.163
r_mcbond_other2.15
r_angle_refined_deg1.531
r_angle_other_deg0.768
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.297
r_dihedral_angle_4_deg21.406
r_dihedral_angle_3_deg11.739
r_dihedral_angle_1_deg6.358
r_mcangle_it3.486
r_mcbond_it2.163
r_mcbond_other2.15
r_angle_refined_deg1.531
r_angle_other_deg0.768
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1675
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing