3F3U | pdb_00003f3u

Kinase domain of cSrc in complex with inhibitor RL37 (Type III)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OIQ	PDB ENTRY 2OIQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	293	10% PEG 4000, 0.05M sodium acetate, 4% glycerol, 0.1M MES , pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.09	α = 78.94
b = 63.53	β = 89.37
c = 73.99	γ = 90.06

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	MARRESEARCH	Dynamically bendable mirror	2008-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.980890	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	40	97.2	0.088	13.15		26052	25330		-3	36.777

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	88.7		0.369	3.6

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 2OIQ	2.5	36.59	26052	25328	1014	100	0.224	0.222	0.22	0.281	0.27	RANDOM	21.642

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]
-0.06	-0.85	0.59	-1.32	0.16	1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.765
r_dihedral_angle_3_deg	19.891
r_dihedral_angle_4_deg	17.79
r_dihedral_angle_1_deg	6.892
r_scangle_it	2.94
r_scbond_it	1.908
r_angle_refined_deg	1.755
r_mcangle_it	1.352
r_mcbond_it	0.792
r_nbtor_refined	0.319
r_symmetry_hbond_refined	0.3
r_symmetry_vdw_refined	0.273
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.108
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4191
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	78

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling