3LTF | pdb_00003ltf

Crystal Structure of the Drosophila Epidermal Growth Factor Receptor ectodomain in complex with Spitz

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I2T	dEGFR domains I-IV (pdb entry 3I2T)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	294	1.5 M sodium potassium phosphate, pH 6.9 4% tert-butanol , VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
4.58	73.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.208	α = 90
b = 124.239	β = 90
c = 186.508	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	ADSC QUANTUM 270	Rh coated Si monochromatic mirrors	2007-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.91790	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.14	40.5	99.8	0.147	10.8	6.1	47481	45880	2	2	68.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.2	3.34	100		0.567	2	6.2	4714

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	dEGFR domains I-IV (pdb entry 3I2T)	3.2	40	2	2	45880	41290	4589	99.79	0.2405	0.2405	0.23664	0.24	0.27542	0.28	RANDOM	80.197

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]
-0.3			0.38		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.155
r_dihedral_angle_3_deg	17.073
r_dihedral_angle_4_deg	15.641
r_dihedral_angle_1_deg	5.464
r_scangle_it	1.374
r_angle_refined_deg	1.126
r_scbond_it	0.74
r_mcangle_it	0.608
r_mcbond_it	0.314
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.155
r_dihedral_angle_3_deg	17.073
r_dihedral_angle_4_deg	15.641
r_dihedral_angle_1_deg	5.464
r_scangle_it	1.374
r_angle_refined_deg	1.126
r_scbond_it	0.74
r_mcangle_it	0.608
r_mcbond_it	0.314
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9014
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	199

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.