3BPU

Crystal structure of the 3rd PDZ domain of human membrane associated guanylate kinase, C677S and C709S double mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.22930.05M Zn acetate pH 6.2, 30% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.141.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.472α = 90
b = 61.578β = 90
c = 80.113γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97912SLSX10SA

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
11.640.0699.90.0740.0317.17.110994104462
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)
11.61.6999.70.8980.3462.27.11571

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 1UJV, 1G9O1.628.74104461044651599.960.204180.202020.25112RANDOM15.883
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]
2.32-0.12-2.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.389
r_dihedral_angle_3_deg11.723
r_dihedral_angle_4_deg10.265
r_scangle_it8.178
r_scbond_it6.953
r_dihedral_angle_1_deg5.983
r_mcangle_it4.862
r_mcbond_it3.592
r_angle_refined_deg1.597
r_mcbond_other1.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.389
r_dihedral_angle_3_deg11.723
r_dihedral_angle_4_deg10.265
r_scangle_it8.178
r_scbond_it6.953
r_dihedral_angle_1_deg5.983
r_mcangle_it4.862
r_mcbond_it3.592
r_angle_refined_deg1.597
r_mcbond_other1.084
r_angle_other_deg0.916
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms630
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing