9RHY | pdb_00009rhy

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		295	Protein solution (70 mg/ml): 40 mM Tris, pH 7.4, 2 mM MgCl2 Well solution: 2.4 M Sodium malonate pH 7.0 Drops: 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.37	α = 90
b = 80.37	β = 90
c = 70.16	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	CCD	MARMOSAIC 225 mm CCD		2014-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97372	ESRF	BM14

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	2.3	19.6	96.4	0.37	0.4	0.15	0.989	13.3	12.9		10321

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)
	2.3	2.38	99.8		1.636	1.86	0.873	0.334	1.6	8.2

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	2.3	19.6	10319	474	96.493	0.178	0.1747	0.1707	0.2479	0.2485	26.873

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]
0.586			0.586		-1.172

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.66
r_dihedral_angle_6_deg	15.29
r_dihedral_angle_2_deg	12.08
r_dihedral_angle_1_deg	7.462
r_lrange_it	5.248
r_lrange_other	5.234
r_scangle_it	3.828
r_scangle_other	3.827
r_scbond_it	2.378
r_scbond_other	2.376
r_angle_refined_deg	2.286
r_mcangle_it	2.063
r_mcangle_other	2.063
r_mcbond_it	1.297
r_mcbond_other	1.286
r_angle_other_deg	0.756
r_nbd_refined	0.225
r_symmetry_nbd_other	0.204
r_nbd_other	0.196
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.105
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.098
r_symmetry_xyhbond_nbd_other	0.024
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1498
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	1

Software

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