3BT2

Structure of urokinase receptor, urokinase and vitronectin complex

X-RAY DIFFRACTION

---

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	8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.096	α = 90
b = 87.205	β = 94.31
c = 124.274	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	ADSC QUANTUM 315			M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.0	APS	24-ID-C
2	SYNCHROTRON	NSLS BEAMLINE X12C	1.0	NSLS	X12C

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	2.5	50	99.2	0.077	0.077	24.1	5.3		38381			42.2

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	2.5	2.59	96		0.356	0.356	2.8	4.1	3675

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	2.5	42.88	37032	1191	99.16	0.22993	0.22862	0.2717	RANDOM	62.232

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]
-0.13		-0.7	1.5		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.001
r_dihedral_angle_4_deg	19.28
r_dihedral_angle_3_deg	18.315
r_dihedral_angle_1_deg	7.848
r_scangle_it	2.926
r_scbond_it	2.001
r_angle_refined_deg	1.74
r_mcangle_it	1.264
r_angle_other_deg	1.11
r_mcbond_it	1.039
r_xyhbond_nbd_other	0.417
r_xyhbond_nbd_refined	0.236
r_nbd_refined	0.227
r_nbd_other	0.213
r_symmetry_vdw_other	0.184
r_nbtor_refined	0.182
r_mcbond_other	0.166
r_symmetry_vdw_refined	0.135
r_chiral_restr	0.122
r_symmetry_hbond_refined	0.121
r_nbtor_other	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003
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	6527
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	70

Software

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