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)
Type	Source	Accession Code	Details
experimental model	PDB	2O88	PDB entry 2o88

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	288	2M 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 coefficient	Solvent content
1.89	34.98

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	BRUKER SMART 6000	Montel Optics	2005-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.85	47.636	92.8	0.0653	0.0653		7.6	10944	10158			17.692

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)	Redundancy	Number Unique Reflections (All)
1	1.85	1.95	72.5		0.2426	0.2649	3.49	1.26	1123

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2o88	1.85	18	10098	998	92.77	0.192	0.185	0.248	RANDOM	16.612

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.555
r_dihedral_angle_4_deg	16.349
r_dihedral_angle_3_deg	15.556
r_dihedral_angle_1_deg	6.363
r_scangle_it	3.849
r_scbond_it	2.825
r_angle_refined_deg	2.106
r_mcangle_it	1.934
r_mcbond_it	1.312
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.555
r_dihedral_angle_4_deg	16.349
r_dihedral_angle_3_deg	15.556
r_dihedral_angle_1_deg	6.363
r_scangle_it	3.849
r_scbond_it	2.825
r_angle_refined_deg	2.106
r_mcangle_it	1.934
r_mcbond_it	1.312
r_nbtor_refined	0.323
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.189
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.151
r_gen_planes_refined	0.014
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1045
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.