3OV1

Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1 M HEPES, 20% w/v Polyethylene Glycol 10,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
1.7827.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.131α = 90
b = 42.131β = 90
c = 108.983γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2010-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.650940.06322.313.712936
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6688.30.1317.513.91181

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 REPLACEMENTTHROUGHOUTPDB entry 3C711.623.041238164595.880.163810.161450.21383RANDOM15.784
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]
-0.03-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.897
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg11.424
r_dihedral_angle_1_deg6.967
r_scangle_it4.668
r_scbond_it3.249
r_angle_refined_deg2.553
r_mcangle_it2.345
r_mcbond_it1.478
r_chiral_restr0.488
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.897
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg11.424
r_dihedral_angle_1_deg6.967
r_scangle_it4.668
r_scbond_it3.249
r_angle_refined_deg2.553
r_mcangle_it2.345
r_mcbond_it1.478
r_chiral_restr0.488
r_bond_refined_d0.03
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms867
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms16

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling