1XDG

X-ray structure of LFA-1 I-domain in complex with LFA878 at 2.1A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	sodium citrate, ammonium acetate, glycerol, PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.2	60.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.9	α = 90
b = 77.4	β = 90
c = 92.3	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MARRESEARCH		1999-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM1A	0.80074	ESRF	BM1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.1	8	98.8	0.067	22.5	4.2	29635	29635

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.17	99.8		0.236	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1CQP	2.1	8	28105	28105	1492	98.3	0.19205	0.19096	0.21276	RANDOM	32.077

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]
0.42			-1.72		1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.032
r_scangle_it	4.362
r_dihedral_angle_1_deg	3.566
r_scbond_it	2.591
r_mcangle_it	1.922
r_angle_refined_deg	1.375
r_mcbond_it	1.077
r_angle_other_deg	0.783
r_symmetry_vdw_other	0.246
r_nbd_refined	0.207
r_nbd_other	0.204
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.127
r_symmetry_hbond_refined	0.125
r_chiral_restr	0.082
r_metal_ion_refined	0.073
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2936
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing