9RIE | pdb_00009rie

Integrin alpha(2) I-domain mutant

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9RI7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	Protein solution (100 mg/ml): 40 mM Tris, pH 7.4, 2 mM MgCl2 Well solution: 0.15 M DL-malic acid, pH 7.0, 20 % PEG 3350 Drops: 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.26	α = 90
b = 53.42	β = 96.093
c = 49.02	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	295	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	1.3	24.53	88.1	0.037	0.052	0.036	0.998	14.8	2.9		39795

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)
	1.3	1.33	37.3		0.502	0.71	0.502	0.433	1.4	1.6

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	1.305	24.53	39783	1982	87.808	0.15	0.1475	0.1424	0.189	0.1816	20.116

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]
-0.278		-0.037	-0.29		0.563

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.833
r_dihedral_angle_6_deg	15.952
r_lrange_other	15.389
r_dihedral_angle_3_deg	13.016
r_scangle_it	10.932
r_scangle_other	10.927
r_mcangle_other	9.039
r_mcangle_it	9.037
r_scbond_it	7.837
r_scbond_other	7.836
r_dihedral_angle_1_deg	6.707
r_mcbond_it	6.534
r_mcbond_other	6.504
r_dihedral_angle_2_deg	5.975
r_rigid_bond_restr	4.706
r_angle_refined_deg	2.093
r_angle_other_deg	0.701
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.219
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.178
r_nbd_other	0.173
r_symmetry_nbd_refined	0.142
r_chiral_restr	0.104
r_symmetry_xyhbond_nbd_other	0.09
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1478
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	10

Software

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