2O88 | pdb_00002o88

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)
Type	Source	Accession Code	Details
experimental model	PDB	1BBZ	PDB ENTRY 1BBZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Capillary counter diffusion	7	293	Ammoniun sulphate, pH 7, Capillary counter diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.17	α = 90
b = 50.093	β = 90
c = 56.431	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	Bruker Microstar micro-focus (Montel Optics)	2006-02-02	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	1.75	50	92.2	0.0682	0.0415	16.43	5.9	13236	13236			19.272

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)	Redundancy	Number Unique Reflections (All)
1	1.75	1.85	75.8		0.2453	0.219	4.41	2.79	1638

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BBZ	1.75	20	12531	13178	647	92.18	0.171	0.169	0.17	0.213	0.22	RANDOM	24.29

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			-0.01		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.415
r_dihedral_angle_4_deg	24.692
r_dihedral_angle_3_deg	14.989
r_dihedral_angle_1_deg	5.543
r_scangle_it	3.443
r_scbond_it	2.361
r_angle_refined_deg	1.744
r_mcangle_it	1.58
r_mcbond_it	1.067
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.415
r_dihedral_angle_4_deg	24.692
r_dihedral_angle_3_deg	14.989
r_dihedral_angle_1_deg	5.543
r_scangle_it	3.443
r_scbond_it	2.361
r_angle_refined_deg	1.744
r_mcangle_it	1.58
r_mcbond_it	1.067
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.301
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.193
r_symmetry_vdw_refined	0.155
r_chiral_restr	0.112
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1037
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	10

Software

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

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.