9RK5 | pdb_00009rk5

Integrin alpha(2) I-domain mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DZI

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: 200 nl of 40% glycerol were added to the drop.

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.22	α = 90
b = 79.22	β = 90
c = 70.41	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	RIGAKU HyPix-6000HE	VariMax mirrors	2022-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.541838

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	1.9	19.57	99.8	0.09	0.099	0.041	0.999	18.9	10.3		18175

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)
	1.9	1.94	100		0.693	0.797	0.389	0.845	3	7.8

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	1.9	19.57	18175	881	99.665	0.185	0.1817	0.1782	0.2424	0.2353	37.585

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]
1.535			1.535		-3.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.69
r_dihedral_angle_3_deg	14.374
r_lrange_it	7.02
r_dihedral_angle_2_deg	6.935
r_lrange_other	6.853
r_dihedral_angle_1_deg	6.501
r_scangle_it	5.15
r_scangle_other	5.121
r_scbond_it	3.513
r_scbond_other	3.494
r_mcangle_other	3.053
r_mcangle_it	3.048
r_mcbond_it	2.317
r_mcbond_other	2.309
r_angle_refined_deg	2.047
r_angle_other_deg	0.68
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.202
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.182
r_symmetry_nbd_refined	0.1
r_nbd_other	0.098
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1503
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	24

Software

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