8B5Y | pdb_00008b5y

SHP2 in complex with allosteric imidazopyrazine inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NWF	4NWF, 4NWG
experimental model	PDB	4NWG	4NWF, 4NWG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293.15	21.00 %w/v PEG 3350, 0.30 M K Form

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.908	α = 90
b = 190.263	β = 90
c = 57.297	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 S 16M		2019-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.999983	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.45	95.13	96	0.185	0.147	0.779	4.6	2.3		97403

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	1.45	1.455	87.6		0.022		1.9

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	4NWF, 4NWG	1.83	95.13	94468	2519	99.57	0.1784	0.1773	0.1868	0.2182	0.2219	RANDOM	33.608

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]
1.58		-0.23	-1.16		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.741
r_dihedral_angle_4_deg	19.436
r_dihedral_angle_3_deg	12.66
r_dihedral_angle_1_deg	6.323
r_angle_refined_deg	1.561
r_angle_other_deg	1.275
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8154
Nucleic Acid Atoms
Solvent Atoms	846
Heterogen Atoms	136

Software

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