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 Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.4
Temperature 293.0
Details 1.53M Potassium phosphate, 0.27M Sodium phosphate, 1% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.78 α = 90
b = 58.45 β = 90
c = 73.74 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2007-06-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.99975 SLS X10SA

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.75 33.71 100.0 0.094 0.094 -- 7.2 22359 22359 0.0 0.0 20.4
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.75 1.84 100.0 0.844 0.844 2.9 7.3 23287

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.75 33.71 -- 0.0 21214 21214 1144 99.92 0.17657 0.17657 0.175 0.20529 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.75 1.795 -- 67 1529 0.224 0.33 -- 99.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.652
Anisotropic B[1][1] 0.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.32
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.877
r_xyhbond_nbd_refined 0.148
r_gen_planes_other 0.001
r_nbtor_other 0.088
r_bond_refined_d 0.012
r_mcangle_it 5.194
r_gen_planes_refined 0.005
r_nbtor_refined 0.166
r_angle_refined_deg 1.404
r_dihedral_angle_2_deg 40.772
r_symmetry_vdw_refined 0.207
r_symmetry_hbond_refined 0.169
r_mcbond_other 1.566
r_bond_other_d 0.002
r_angle_other_deg 1.913
r_dihedral_angle_3_deg 11.648
r_scangle_it 10.02
r_chiral_restr 0.088
r_mcbond_it 3.711
r_symmetry_vdw_other 0.315
r_scbond_it 7.164
r_dihedral_angle_4_deg 9.689
r_nbd_other 0.196
r_nbd_refined 0.188
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1513
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 124

Software

Software
Software Name Purpose
REFMAC refinement version: 5.3.0040
MAR345 data collection version: CCD
MOSFLM data reduction
SCALA data scaling
PHASER phasing