3EG3

Crystal structure of the N114A mutant of ABL-SH3 domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ABQPDB entry 1ABQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP32882M ammonium sulphate, 5% PEG300, 10% glycerol, and 0.1 M of buffer solution, vapor diffusion, hanging drop, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
1.7630.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.819α = 90
b = 53.096β = 90
c = 41.296γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000Montel Optics2006-01-19MSINGLE 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
11.3541.3192.30.03280.03286.79111621030312.829
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)
11.351.4582.20.13260.13267.331734

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 1ABQ1.413.77938044293.680.210.2080.24RANDOM15.844
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]
-0.020.07-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.061
r_dihedral_angle_3_deg11.185
r_dihedral_angle_4_deg11.097
r_dihedral_angle_1_deg7.659
r_scangle_it3.78
r_scbond_it3.335
r_mcangle_it2.174
r_angle_refined_deg2.097
r_mcbond_it1.432
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.061
r_dihedral_angle_3_deg11.185
r_dihedral_angle_4_deg11.097
r_dihedral_angle_1_deg7.659
r_scangle_it3.78
r_scbond_it3.335
r_mcangle_it2.174
r_angle_refined_deg2.097
r_mcbond_it1.432
r_nbtor_refined0.317
r_symmetry_vdw_refined0.273
r_xyhbond_nbd_refined0.241
r_nbd_refined0.236
r_symmetry_hbond_refined0.228
r_chiral_restr0.12
r_bond_refined_d0.014
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms491
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms6

Software

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