2I9B | pdb_00002i9b

Crystal structure of ATF-urokinase receptor complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YWH	PDB ENTRY 1YWH, 2I9A
experimental model	PDB	2I9A	PDB ENTRY 1YWH, 2I9A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	22.5% w/v PEG3350, 200 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.914	α = 90
b = 281.921	β = 105.41
c = 62.811	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	MAR CCD 225 mm		2005-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0000	APS	22-BM

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	2.8	50	91.2	0.046	17.6	2.8	47048	47048		-3

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	2.8	2.9	51.3		0.206	2.44	1.8	2636

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1YWH, 2I9A	2.8	15	44793	1911	91.18	0.22372	0.22194	0.2206	0.26498	0.2639	RANDOM	67.301

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]
3.8		2.52	-3.9		1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.459
r_scangle_it	18.474
r_scbond_it	15.956
r_dihedral_angle_3_deg	14.196
r_mcangle_it	12.726
r_dihedral_angle_4_deg	12.344
r_mcbond_it	9.938
r_dihedral_angle_1_deg	2.877
r_angle_refined_deg	1.888
r_nbtor_refined	0.314
r_symmetry_hbond_refined	0.272
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.208
r_symmetry_vdw_refined	0.179
r_chiral_restr	0.131
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11696
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing