8XPV | pdb_00008xpv

The Crystal Structure of EphA2 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8BOM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Sodium Acetate, 0.1M Sodium Cacodylate HCl pH6.5, 18% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.931	α = 90
b = 107.504	β = 108.686
c = 40.691	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 PILATUS 6M		2023-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1	SPring-8	BL45XU

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	1.55	38.576	97.8	0.087	11.7	5.3		37926

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	1.55	1.58			0.844

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	1.55	38.576	37891	1935	97.69	0.165	0.1641	0.18	0.1903	0.2	17.476

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]
-0.541		-0.257	1.073		-0.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.154
r_dihedral_angle_6_deg	15.769
r_dihedral_angle_3_deg	12.714
r_dihedral_angle_1_deg	5.934
r_lrange_it	5.092
r_lrange_other	4.809
r_scangle_it	2.819
r_scangle_other	2.819
r_mcangle_it	1.941
r_mcangle_other	1.941
r_scbond_it	1.684
r_scbond_other	1.683
r_mcbond_it	1.141
r_mcbond_other	1.136
r_angle_refined_deg	1.114
r_angle_other_deg	0.405
r_symmetry_nbd_refined	0.215
r_nbd_refined	0.206
r_nbd_other	0.186
r_nbtor_refined	0.181
r_symmetry_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.164
r_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.059
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2136
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	57

Software

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