1YWH | pdb_00001ywh

crystal structure of urokinase plasminogen activator receptor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	ammonium sulfate, imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 20K

Crystal Properties
Matthews coefficient	Solvent content
3.6	66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.928	α = 90
b = 136.831	β = 97.27
c = 140.536	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	110	CCD	ADSC QUANTUM 4		2002-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.934	ESRF	ID14-2

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	2.7	24.85	99.5	0.09	12.4			110121	1	1

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	2.7	2.769	97.3		0.575	2.61

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	OMIT MAPs	2.7	24.85	106866	101531	5335	97.19	0.24876	0.24876	0.24524	0.281	0.31526	0.3475	RANDOM	58.796

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		0.12	-0.17		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.625
r_dihedral_angle_3_deg	22.192
r_dihedral_angle_4_deg	18.176
r_dihedral_angle_1_deg	7.876
r_scangle_it	2.188
r_angle_refined_deg	1.634
r_scbond_it	1.327
r_mcangle_it	0.94
r_mcbond_it	0.497
r_nbtor_refined	0.311
r_nbd_refined	0.232
r_symmetry_hbond_refined	0.219
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.112
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16900
Nucleic Acid Atoms
Solvent Atoms	749
Heterogen Atoms	903

Software

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