6G8W

Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RLE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.151.4M Na/K phosphate pH 8.2
Crystal Properties
Matthews coefficientSolvent content
2.2946.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.825α = 90
b = 82.613β = 110.82
c = 49.22γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2011-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.1226.8599.30.07815.784.110762
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.122.181000.6260.9992.974.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3RLE2.1226.851022253899.440.188390.185970.23548RANDOM32.953
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]
3.41-1.97-1.34-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.69
r_dihedral_angle_3_deg15.222
r_dihedral_angle_4_deg11.986
r_long_range_B_refined8.959
r_long_range_B_other8.957
r_dihedral_angle_1_deg6.663
r_scangle_other6.299
r_mcangle_it5.09
r_mcangle_other5.088
r_scbond_it4.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.69
r_dihedral_angle_3_deg15.222
r_dihedral_angle_4_deg11.986
r_long_range_B_refined8.959
r_long_range_B_other8.957
r_dihedral_angle_1_deg6.663
r_scangle_other6.299
r_mcangle_it5.09
r_mcangle_other5.088
r_scbond_it4.063
r_scbond_other4.061
r_mcbond_other3.356
r_mcbond_it3.355
r_angle_refined_deg1.979
r_angle_other_deg1.143
r_chiral_restr0.106
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1370
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing