4GLY | pdb_00004gly

Human urokinase-type plasminogen activator uPA in complex with the two-disulfide bridge peptide UK504

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	1.8M Ammonium sulfate, 5% PEG400, 0.05% Sodium azide, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.8	α = 90
b = 120.8	β = 90
c = 43.08	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2012-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

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	1.518	29.13	100	0.099		4.6	36222	36222	6	3	12.3

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	1.518	1.6	100		0.318	3.8	4.6	5284

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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 2NWN	1.518	29.13	3	6	36227	34197	1784	99.33	0.1318	0.12808	0.13	0.20416	0.2	RANDOM	18.622

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]
-0.08	-0.08		-0.08		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	52.906
r_dihedral_angle_2_deg	36.166
r_dihedral_angle_4_deg	22.142
r_sphericity_bonded	20.461
r_dihedral_angle_3_deg	13.744
r_dihedral_angle_1_deg	6.86
r_rigid_bond_restr	5.64
r_angle_refined_deg	1.996
r_chiral_restr	0.16
r_bond_refined_d	0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	52.906
r_dihedral_angle_2_deg	36.166
r_dihedral_angle_4_deg	22.142
r_sphericity_bonded	20.461
r_dihedral_angle_3_deg	13.744
r_dihedral_angle_1_deg	6.86
r_rigid_bond_restr	5.64
r_angle_refined_deg	1.996
r_chiral_restr	0.16
r_bond_refined_d	0.02
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2032
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	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.