2Q3G

Structure of the PDZ domain of human PDLIM7 bound to a C-terminal extension from human beta-tropomyosin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.1M HEPES; 10% isopropanol; 20% PEG 4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9637.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.052α = 90
b = 55.404β = 90
c = 57.316γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9182SLSX10SA

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
11.1139.8499.40.0420.0385.15868158329
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)
1.111.151000.1440.121114.6

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 REPLACEMENTTHROUGHOUThomoly based model1.1139.845868155322294699.40.132720.132720.131430.15679RANDOM7.247
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]
-0.180.010.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.656
r_dihedral_angle_1_deg26.903
r_dihedral_angle_4_deg22.579
r_dihedral_angle_3_deg10.618
r_sphericity_free7.214
r_scangle_it3.471
r_sphericity_bonded3.269
r_scbond_it2.667
r_mcangle_it2.248
r_angle_refined_deg1.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.656
r_dihedral_angle_1_deg26.903
r_dihedral_angle_4_deg22.579
r_dihedral_angle_3_deg10.618
r_sphericity_free7.214
r_scangle_it3.471
r_sphericity_bonded3.269
r_scbond_it2.667
r_mcangle_it2.248
r_angle_refined_deg1.69
r_mcbond_it1.622
r_angle_other_deg1.465
r_rigid_bond_restr1.211
r_mcbond_other0.587
r_symmetry_vdw_other0.279
r_nbd_refined0.224
r_nbd_other0.208
r_nbtor_refined0.178
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.173
r_symmetry_vdw_refined0.133
r_chiral_restr0.113
r_nbtor_other0.091
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1405
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing