9KL4 | pdb_00009kl4

Crystal structure of EGFR complexed with N-[4-[4-amino-6-ethynyl-5-(3-quinolyl)pyrrolo[2,3-d]pyrimidin-7-yl]norbornan-1-yl]pyrimidine-5-carboxamide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Analysis by outsourcing.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	1.2 M K/Na-tartrate, 0.1 M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.92	α = 90
b = 146.92	β = 90
c = 146.92	γ = 90

Symmetry
Space Group	I 2 3

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 EIGER X 16M		2020-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99981	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.32	103.89	100	1	21.8	24.7		22851

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.32	2.37	100		0.607

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	Analysis by outsourcing.	2.32	103.89	21538	1296	100	0.18863	0.18565	0.191	0.23801	0.2406	RANDOM	79.282

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.668
r_long_range_B_other	21.106
r_long_range_B_refined	21.104
r_scangle_other	18.562
r_mcangle_other	16.486
r_mcangle_it	16.483
r_scbond_it	14.223
r_scbond_other	14.217
r_dihedral_angle_4_deg	13.699
r_dihedral_angle_3_deg	13.106
r_mcbond_it	12.919
r_mcbond_other	12.907
r_dihedral_angle_1_deg	6.665
r_angle_refined_deg	1.584
r_angle_other_deg	1.242
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2504
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	39

Software

Software
Software Name	Purpose
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
Aimless	data scaling
REFMAC	refinement