9HMI | pdb_00009hmi

Crystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2 peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M ammonium formate; 20% polyethylene glycol 3350 (wt/vol)

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.977	α = 90
b = 69.231	β = 90
c = 137.828	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	PIXEL	DECTRIS PILATUS3 6M		2021-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.99	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.78	50.338	97.6	0.2	0.21	0.06	0.997	7.3	4.4		12325

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.78	2.93			1.6	0.9	0.9	0.15	0.4

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.87	50.338	12249	621	98.102	0.235	0.2327	0.5662	0.2805	0.6002	RANDOM	99.374

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]
-3.939			3.333		0.606

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	25.863
r_scangle_it	19.849
r_dihedral_angle_3_deg	18.19
r_mcangle_it	16.577
r_dihedral_angle_6_deg	13.91
r_scbond_it	13.106
r_mcbond_it	10.8
r_dihedral_angle_1_deg	9.077
r_dihedral_angle_2_deg	7.037
r_angle_refined_deg	2.182
r_nbtor_refined	0.318
r_symmetry_nbd_refined	0.309
r_nbd_refined	0.272
r_symmetry_xyhbond_nbd_refined	0.225
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.155
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2795
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms

Software

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