9RI7 | pdb_00009ri7

Integrin alpha(2) I-domain mutant

X-RAY DIFFRACTION

---

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 (55 mg/ml): 40 mM Tris, pH 7.4, 2 mM MgCl2 Well solution: 0.1 M succinic acid, pH 7.0, 15 % PEG 3350 Drops: 2:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.03	α = 90
b = 53.76	β = 100.62
c = 44.65	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	CCD	MARMOSAIC 225 mm CCD		2013-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97372	ESRF	ID29

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	19.19	94.6	0.046	0.064	0.046	0.999	13.2	3.1		21566

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	80		1.004	1.419	1.004	0.415	1	3

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	19.19	21566	1084	94.472	0.163	0.1608	0.1534	0.2002	0.1887	21.839

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]
-0.068		-0.089	-1.242		1.255

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.891
r_dihedral_angle_3_deg	12.619
r_dihedral_angle_2_deg	7.912
r_dihedral_angle_1_deg	6.902
r_lrange_it	5.589
r_lrange_other	5.418
r_scangle_it	3.633
r_scangle_other	3.631
r_scbond_it	2.83
r_scbond_other	2.829
r_angle_refined_deg	2.27
r_mcangle_it	1.986
r_mcangle_other	1.986
r_mcbond_it	1.336
r_mcbond_other	1.326
r_angle_other_deg	0.76
r_xyhbond_nbd_refined	0.266
r_nbd_refined	0.218
r_nbd_other	0.199
r_symmetry_nbd_other	0.193
r_symmetry_nbd_refined	0.188
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_other	0.178
r_symmetry_xyhbond_nbd_refined	0.154
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	62

Software

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