3B76

Crystal structure of the third PDZ domain of human ligand-of-numb protein-X (LNX1) in complex with the C-terminal peptide from the coxsackievirus and adenovirus receptor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42931.53M Potassium phosphate, 0.27M Sodium phosphate, 1% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.782α = 90
b = 58.449β = 90
c = 73.741γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99975SLSX10SA

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
11.7533.711000.0940.094167.2223592235920.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.841000.8440.8442.97.323287

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 entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L1.7533.712121421214114499.920.176570.176570.1750.20529RANDOM17.652
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]
0.56-0.880.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.772
r_dihedral_angle_3_deg11.648
r_scangle_it10.02
r_dihedral_angle_4_deg9.689
r_scbond_it7.164
r_dihedral_angle_1_deg5.877
r_mcangle_it5.194
r_mcbond_it3.711
r_angle_other_deg1.913
r_mcbond_other1.566
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.772
r_dihedral_angle_3_deg11.648
r_scangle_it10.02
r_dihedral_angle_4_deg9.689
r_scbond_it7.164
r_dihedral_angle_1_deg5.877
r_mcangle_it5.194
r_mcbond_it3.711
r_angle_other_deg1.913
r_mcbond_other1.566
r_angle_refined_deg1.404
r_symmetry_vdw_other0.315
r_symmetry_vdw_refined0.207
r_nbd_other0.196
r_nbd_refined0.188
r_symmetry_hbond_refined0.169
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.148
r_chiral_restr0.088
r_nbtor_other0.088
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1513
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing