3BT1

Structure of urokinase receptor, urokinase and vitronectin complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FD6	PDB ENTRY 2FD6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7.5	295	12% PEG 3350, 50mM HEPES pH 7.5, MICRODIALYSIS, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.353	α = 90
b = 105.187	β = 90
c = 55.36	γ = 90

Symmetry
Space Group	P 21 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 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	100	99.5	0.081	0.081	33.1	5.9		14540			82

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	100		0.803	0.803	2.6	5.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2FD6	2.8	27.68	13778	726	99.6	0.244	0.241	0.308	RANDOM	54.32

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]
0.48			-3.25		2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.371
r_dihedral_angle_3_deg	21.248
r_dihedral_angle_4_deg	19.56
r_dihedral_angle_1_deg	9.464
r_scangle_it	2.154
r_angle_refined_deg	1.821
r_scbond_it	1.356
r_angle_other_deg	1.048
r_mcangle_it	0.958
r_mcbond_it	0.746
r_nbd_refined	0.266
r_symmetry_vdw_other	0.246
r_nbd_other	0.221
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.191
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_other	0.163
r_mcbond_other	0.105
r_chiral_restr	0.102
r_nbtor_other	0.1
r_symmetry_hbond_refined	0.064
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3394
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing