2OPG

The crystal structure of the 10th PDZ domain of MPDZ


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1M BIS-TRIS, 20% mPEG 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4648.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.944α = 90
b = 54.944β = 90
c = 118.355γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97880SLSX10SA

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
11.539.4799.90.06819.28.43389033890
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)
1.51.5899.60.4557.34827

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 REPLACEMENTTHROUGHOUTPDB entry 2FNE1.539.473215032150171899.810.174730.174730.172440.21718RANDOM18.291
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]
0.270.130.27-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.58
r_dihedral_angle_4_deg19.421
r_dihedral_angle_3_deg12.734
r_scangle_it7.195
r_dihedral_angle_1_deg6.56
r_scbond_it5.291
r_mcangle_it3.903
r_mcbond_it2.537
r_angle_refined_deg1.929
r_angle_other_deg1.332
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.58
r_dihedral_angle_4_deg19.421
r_dihedral_angle_3_deg12.734
r_scangle_it7.195
r_dihedral_angle_1_deg6.56
r_scbond_it5.291
r_mcangle_it3.903
r_mcbond_it2.537
r_angle_refined_deg1.929
r_angle_other_deg1.332
r_mcbond_other0.754
r_symmetry_vdw_other0.358
r_symmetry_vdw_refined0.266
r_symmetry_hbond_refined0.241
r_nbd_other0.218
r_nbd_refined0.198
r_chiral_restr0.192
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.173
r_nbtor_other0.09
r_bond_refined_d0.021
r_gen_planes_refined0.008
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1529
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing