3EG1

Crystal structure of the N114Q mutant of ABL-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O88PDB entry 2o88

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.52882M ammonium sulphate, 0.4 M NaCl, 0.1 M sodium citrate, 10% glycerol, pH 3.5, vapor diffusion, hanging drop, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
1.8934.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.996α = 90
b = 47.636β = 90
c = 55.662γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000Montel Optics2005-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54

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
11.8547.63692.80.06530.06537.6109441015817.692
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)
11.851.9572.50.24260.26493.491.261123

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 2o881.85181009899892.770.1920.1850.248RANDOM16.612
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]
0.14-0.09-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.555
r_dihedral_angle_4_deg16.349
r_dihedral_angle_3_deg15.556
r_dihedral_angle_1_deg6.363
r_scangle_it3.849
r_scbond_it2.825
r_angle_refined_deg2.106
r_mcangle_it1.934
r_mcbond_it1.312
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.555
r_dihedral_angle_4_deg16.349
r_dihedral_angle_3_deg15.556
r_dihedral_angle_1_deg6.363
r_scangle_it3.849
r_scbond_it2.825
r_angle_refined_deg2.106
r_mcangle_it1.934
r_mcbond_it1.312
r_nbtor_refined0.323
r_nbd_refined0.228
r_symmetry_hbond_refined0.189
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.156
r_chiral_restr0.151
r_gen_planes_refined0.014
r_bond_refined_d0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1045
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms10

Software

Software
Software NamePurpose
SAINTdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
SCALAdata scaling