2QG1

Crystal structure of the 11th PDZ domain of MPDZ (MUPP1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HE2PDB entries 2HE2, 1TP3
experimental modelPDB 1TP3PDB entries 2HE2, 1TP3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42930.8M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.409α = 90
b = 36.919β = 90
c = 63.609γ = 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
11.431.896.60.0730.07313.54.61550115501
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)
1.41.4894.70.3940.3942.63.88319

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 entries 2HE2, 1TP31.431.8146861468678096.160.172520.172520.169370.23418RANDOM14.93
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]
0.72-1.841.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.514
r_dihedral_angle_4_deg15.867
r_sphericity_free12.968
r_dihedral_angle_3_deg12.69
r_scangle_it9.261
r_scbond_it7.792
r_sphericity_bonded6.723
r_mcangle_it6.359
r_dihedral_angle_1_deg5.724
r_mcbond_it5.557
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.514
r_dihedral_angle_4_deg15.867
r_sphericity_free12.968
r_dihedral_angle_3_deg12.69
r_scangle_it9.261
r_scbond_it7.792
r_sphericity_bonded6.723
r_mcangle_it6.359
r_dihedral_angle_1_deg5.724
r_mcbond_it5.557
r_rigid_bond_restr4.205
r_mcbond_other3.847
r_angle_refined_deg1.489
r_angle_other_deg0.865
r_symmetry_vdw_refined0.259
r_symmetry_vdw_other0.23
r_symmetry_hbond_refined0.222
r_nbd_refined0.208
r_nbd_other0.194
r_nbtor_refined0.162
r_xyhbond_nbd_refined0.162
r_nbtor_other0.09
r_chiral_restr0.086
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms667
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing