2O88

Crystal structure of the N114A 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 1BBZPDB ENTRY 1BBZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Capillary counter diffusion7293Ammoniun sulphate, pH 7, Capillary counter diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2946.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.17α = 90
b = 50.093β = 90
c = 56.431γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000Bruker Microstar micro-focus (Montel Optics)2006-02-02MSINGLE 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
11.755092.20.06820.041516.435.9132361323619.272
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)
11.751.8575.80.24530.2194.412.791638

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 ENTRY 1BBZ1.7520125311317864792.180.1710.1690.213RANDOM24.29
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]
-0.17-0.010.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.415
r_dihedral_angle_4_deg24.692
r_dihedral_angle_3_deg14.989
r_dihedral_angle_1_deg5.543
r_scangle_it3.443
r_scbond_it2.361
r_angle_refined_deg1.744
r_mcangle_it1.58
r_mcbond_it1.067
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.415
r_dihedral_angle_4_deg24.692
r_dihedral_angle_3_deg14.989
r_dihedral_angle_1_deg5.543
r_scangle_it3.443
r_scbond_it2.361
r_angle_refined_deg1.744
r_mcangle_it1.58
r_mcbond_it1.067
r_nbtor_refined0.312
r_symmetry_hbond_refined0.301
r_nbd_refined0.206
r_xyhbond_nbd_refined0.193
r_symmetry_vdw_refined0.155
r_chiral_restr0.112
r_gen_planes_refined0.009
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1037
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms10

Software

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