3GSL

Crystal structure of PSD-95 tandem PDZ domains 1 and 2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727735% v/v 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.0. 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4850.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.244α = 90
b = 62.511β = 99.25
c = 59.342γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 270Toroidal focusing mirror2009-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A0.97000NSLSX6A

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
12.055098.10.05821.23.7261122561635.16
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)
2.052.1296.30.3493.13.62594

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entries 2I1N, 2FE52.0532.312561625598257698.090.22090.214120.28146RANDOM37.914
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]
-0.040.07-1.181.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.674
r_dihedral_angle_3_deg10.015
r_dihedral_angle_4_deg9.212
r_scangle_it8.465
r_scbond_it5.924
r_dihedral_angle_1_deg3.94
r_mcangle_it3.827
r_mcbond_it2.631
r_angle_refined_deg0.631
r_symmetry_vdw_refined0.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.674
r_dihedral_angle_3_deg10.015
r_dihedral_angle_4_deg9.212
r_scangle_it8.465
r_scbond_it5.924
r_dihedral_angle_1_deg3.94
r_mcangle_it3.827
r_mcbond_it2.631
r_angle_refined_deg0.631
r_symmetry_vdw_refined0.331
r_nbtor_refined0.328
r_nbd_refined0.275
r_symmetry_hbond_refined0.234
r_xyhbond_nbd_refined0.196
r_chiral_restr0.054
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2864
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms

Software

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