1MFL

The Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MFGPDB ENTRY 1MFG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529223-26% PEG 4000, 20% GLYCEROL, 100mM AMMONIUM ACETATE, 100mM SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.0339.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 26.526α = 90
b = 56.995β = 99.16
c = 30.951γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMIRRORS2002-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.8830.6950.0280.02844.73.7371967068-313
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)
1.881.9590.20.0960.09613.33.34660

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 1MFG1.8830.5770686738330950.1690.1690.16680.2159RANDOM18.168
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]
-0.93-0.240.350.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.462
r_scangle_it5.323
r_scbond_it3.033
r_mcangle_it1.828
r_angle_refined_deg1.579
r_mcbond_it0.977
r_angle_other_deg0.83
r_symmetry_vdw_other0.346
r_nbd_other0.258
r_nbd_refined0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.462
r_scangle_it5.323
r_scbond_it3.033
r_mcangle_it1.828
r_angle_refined_deg1.579
r_mcbond_it0.977
r_angle_other_deg0.83
r_symmetry_vdw_other0.346
r_nbd_other0.258
r_nbd_refined0.22
r_xyhbond_nbd_refined0.184
r_symmetry_hbond_refined0.171
r_symmetry_vdw_refined0.161
r_chiral_restr0.088
r_nbtor_other0.087
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms767
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement