2FD6 | pdb_00002fd6

Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	6.5	298	4% PEG4000, 5% ethylene glycol, 5% methanol, 0.05% sodium azide, 50 mM cacodylate, pH 6.5, MICRODIALYSIS, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.792	α = 90
b = 86.805	β = 94.54
c = 124.69	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	90	CCD	MARRESEARCH		2005-04-09	M	SINGLE WAVELENGTH
2	1		CCD
3	1		CCD
4	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID
2	SYNCHROTRON	NSLS BEAMLINE X25	1.00	NSLS	X25
3	SYNCHROTRON	NSLS BEAMLINE X12C	1.0	NSLS	X12C
4	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.85	41.36	94.5	0.064	16.1			86852			21

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	2.08	77.5		0.338	1.97

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2FAT	1.9	41.36	86852	83101	4228	95.8	0.239	0.239	0.239	0.24	0.276	RANDOM	32.9

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]
-0.31		-3.7	4.95		-4.64

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.2
c_angle_deg	1.5
c_improper_angle_d	0.9
c_bond_d	0.007
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6139
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms	125

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.