9RK7 | pdb_00009rk7

Integrin alpha(2) I-domain mutant

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9RK5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	Protein solution (16.5 mg/ml): 40 mM Tris-HCl (pH 7.4), 2 mM MgCl2 Well solution: 1.92 ammonium suplhate, 0.096 M Bis-Tris, pH 5.5 Drop: 300 nl (protein) + 150 nl (well solution) Cryo: 250 nl of 40% glycerol were added to the drop.

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.55	α = 90
b = 78.55	β = 90
c = 70.48	γ = 90

Symmetry
Space Group	P 42 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 6M		2022-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.88560	ESRF	ID23-1

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	1.6	24.88	99.9	0.146	0.163	0.071	0.994	8.1	9.5		29652

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)
	1.6	1.63	99.8		1.148	1.384	0.761	0.825	1.3	5.7

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	1.6	24.88	29652	1489	99.822	0.198	0.195	0.196	0.2478	0.248	28.275

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]
2.516			2.516		-5.032

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.058
r_dihedral_angle_3_deg	13.779
r_lrange_it	6.809
r_lrange_other	6.691
r_dihedral_angle_1_deg	6.623
r_dihedral_angle_2_deg	5.407
r_scangle_it	4.052
r_scangle_other	3.973
r_scbond_it	2.698
r_scbond_other	2.646
r_angle_refined_deg	2.265
r_mcangle_it	1.988
r_mcangle_other	1.987
r_mcbond_it	1.421
r_mcbond_other	1.42
r_angle_other_deg	0.813
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.223
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.144
r_chiral_restr	0.133
r_nbd_other	0.104
r_symmetry_nbd_refined	0.095
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1496
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	17

Software

Software
Software Name	Purpose
XSCALE	data scaling
Aimless	data scaling
PHASER	phasing
REFMAC	refinement