8PYK | pdb_00008pyk

Human IGF1R with inhibitor 47

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		IGF1R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1 M HEPES pH 7.5-8.5, 9-12 % PEG3350, 5 mM CoCl2, 5 mM CdCl2, 5 mM MgCl2, and 5 mM NiCl2

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.537	α = 90
b = 69.537	β = 90
c = 140.442	γ = 90

Symmetry
Space Group	P 43 21 2

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 PILATUS 2M		2017-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999	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	2.23	17562	100	0.07	24.5	12.7		223284

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	2.23	2.35			1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.23	21.134	17467	872	99.806	0.201	0.198	0.2	0.2526	0.25	68.62

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]
0.53			0.53		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.754
r_dihedral_angle_3_deg	17.675
r_dihedral_angle_4_deg	17.026
r_dihedral_angle_1_deg	7.765
r_lrange_it	7.615
r_lrange_other	7.609
r_scangle_other	4.126
r_scangle_it	4.123
r_mcangle_it	3.499
r_mcangle_other	3.499
r_scbond_it	2.626
r_scbond_other	2.613
r_mcbond_it	2.179
r_mcbond_other	2.166
r_angle_refined_deg	1.861
r_angle_other_deg	1.287
r_symmetry_metal_ion_refined	0.635
r_symmetry_xyhbond_nbd_refined	0.318
r_nbd_other	0.247
r_xyhbond_nbd_refined	0.222
r_nbd_refined	0.216
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.171
r_symmetry_nbd_refined	0.12
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.082
r_metal_ion_refined	0.072
r_bond_refined_d	0.012
r_xyhbond_nbd_other	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2186
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing