3EG2

Crystal structure of the N114Q mutant of ABL-SH3 domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EG3PDB entry 3EG3

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
1.7328.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.679α = 90
b = 52.998β = 90
c = 41.101γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000Montel Optics2006-03-09MSINGLE 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
11.841.10191.30.04280.04286.134769435416.17
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)
11.81.967.90.18050.18053.881.11471

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 3EG31.813.25433630491.260.2120.2080.268RANDOM16.699
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]
-0.030.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.392
r_dihedral_angle_4_deg25.55
r_dihedral_angle_3_deg14.486
r_dihedral_angle_1_deg7.598
r_scangle_it4.926
r_scbond_it3.81
r_mcangle_it2.148
r_angle_refined_deg2.061
r_mcbond_it1.435
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.392
r_dihedral_angle_4_deg25.55
r_dihedral_angle_3_deg14.486
r_dihedral_angle_1_deg7.598
r_scangle_it4.926
r_scbond_it3.81
r_mcangle_it2.148
r_angle_refined_deg2.061
r_mcbond_it1.435
r_nbtor_refined0.315
r_symmetry_vdw_refined0.299
r_symmetry_hbond_refined0.292
r_nbd_refined0.226
r_xyhbond_nbd_refined0.19
r_chiral_restr0.132
r_bond_refined_d0.011
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms495
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms6

Software

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