2HE2

Crystal structure of the 3rd PDZ domain of human discs large homologue 2, DLG2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TP5Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9.
experimental modelPDB 1TP3Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9.
experimental modelPDB 1BFESwissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9.
experimental modelPDB 1BE9Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29325.5% PEG 3350; 0.17M (NH4)2SO4; 15% glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.155α = 90
b = 56.07β = 90
c = 60.472γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97646SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.55098.830918
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5597.5

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 REPLACEMENTTHROUGHOUTSwissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9.1.541.132928129281155998.790.129870.129870.126860.18688RANDOM9.045
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]
-0.32-0.030.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.522
r_dihedral_angle_4_deg15.536
r_dihedral_angle_3_deg11.168
r_sphericity_free9.239
r_scangle_it7.254
r_dihedral_angle_1_deg5.921
r_scbond_it5.844
r_sphericity_bonded4.868
r_mcangle_it4.512
r_mcbond_it4.032
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.522
r_dihedral_angle_4_deg15.536
r_dihedral_angle_3_deg11.168
r_sphericity_free9.239
r_scangle_it7.254
r_dihedral_angle_1_deg5.921
r_scbond_it5.844
r_sphericity_bonded4.868
r_mcangle_it4.512
r_mcbond_it4.032
r_rigid_bond_restr2.738
r_mcbond_other2.556
r_angle_refined_deg1.324
r_angle_other_deg0.858
r_symmetry_vdw_other0.377
r_symmetry_vdw_refined0.264
r_nbd_refined0.202
r_symmetry_hbond_refined0.198
r_nbd_other0.192
r_xyhbond_nbd_refined0.182
r_nbtor_refined0.169
r_nbtor_other0.083
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1546
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing