2FCF

The crystal structure of the 7th PDZ domain of MPDZ (MUPP-1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429830% mPEG 2K, 0.10M KSCN, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.141.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.122α = 90
b = 43.801β = 90
c = 50.167γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.90010SLSX10SA

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
11.7632.99950.0730.0736.8494758968
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)
11.761.8596.30.09550.1849.576.351354

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 REPLACEMENTTHROUGHOUT1n7f1.7632.999475896846295.580.209370.209370.207670.24396RANDOM39.847
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]
-1.713.36-1.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.481
r_dihedral_angle_4_deg13.785
r_dihedral_angle_3_deg12.56
r_scangle_it7.737
r_dihedral_angle_1_deg5.387
r_scbond_it5.321
r_mcangle_it3.87
r_mcbond_it3.124
r_angle_refined_deg1.503
r_angle_other_deg0.877
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.481
r_dihedral_angle_4_deg13.785
r_dihedral_angle_3_deg12.56
r_scangle_it7.737
r_dihedral_angle_1_deg5.387
r_scbond_it5.321
r_mcangle_it3.87
r_mcbond_it3.124
r_angle_refined_deg1.503
r_angle_other_deg0.877
r_mcbond_other0.815
r_symmetry_vdw_other0.265
r_nbd_refined0.21
r_nbd_other0.206
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.14
r_chiral_restr0.09
r_symmetry_hbond_refined0.09
r_nbtor_other0.086
r_symmetry_vdw_refined0.067
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms663
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms

Software

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