5SYS | pdb_00005sys

c-Src V281C bound to N-[3-({6-[(1E)-2-cyano-3-(methylamino)-3-oxoprop-1-en-1-yl]-7-(2-methoxyethyl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl}ethynyl)-4-methylphenyl]-3-(trifluoromethyl)benzamide inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UQG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	100 mM MES pH 6, 8% PEG 3350, 10 mM NaOAc, 14% glycerol, 10 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.813	α = 77.87
b = 63.857	β = 90.1
c = 75.625	γ = 89.83

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	100	PIXEL	DECTRIS PILATUS3 S 6M		2016-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.8	73.94	86.6	0.176	0.209	0.111	0.987	5.7	3.3		16285

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.97	85.6		1.334	1.578	0.833	0.498		3.3	2595

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3uqg	2.8	73.94	15434	827	86.49	0.2881	0.2857	0.29	0.3339	0.33	RANDOM	64.488

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]
-0.61	0.24	-0.06	-2.41	1.23	3.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.574
r_dihedral_angle_3_deg	16.381
r_dihedral_angle_4_deg	15.435
r_dihedral_angle_1_deg	7.117
r_mcangle_it	6.592
r_mcbond_it	3.853
r_mcbond_other	3.852
r_angle_refined_deg	1.423
r_angle_other_deg	0.965
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.574
r_dihedral_angle_3_deg	16.381
r_dihedral_angle_4_deg	15.435
r_dihedral_angle_1_deg	7.117
r_mcangle_it	6.592
r_mcbond_it	3.853
r_mcbond_other	3.852
r_angle_refined_deg	1.423
r_angle_other_deg	0.965
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4128
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

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.