3P70

Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.243	α = 72.57
b = 68.227	β = 84.05
c = 98.972	γ = 80.45

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	MARMOSAIC 225 mm CCD		2010-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

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	2.55	64.42	94.6	0.08	10.8	3.6	49833	47142

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	2.55	2.69	94.1		0.426	2.7	3.6	6841

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	1PPB	2.55	61.28	44784	2384	94.64	0.2105	0.20685	0.27881	RANDOM	54.748

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]
-0.02	0.03	-0.01	0.1		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.015
r_dihedral_angle_3_deg	20.398
r_dihedral_angle_4_deg	18.549
r_dihedral_angle_1_deg	7.408
r_scangle_it	3.091
r_scbond_it	1.996
r_angle_refined_deg	1.841
r_mcangle_it	1.186
r_mcbond_it	0.636
r_chiral_restr	0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.015
r_dihedral_angle_3_deg	20.398
r_dihedral_angle_4_deg	18.549
r_dihedral_angle_1_deg	7.408
r_scangle_it	3.091
r_scbond_it	1.996
r_angle_refined_deg	1.841
r_mcangle_it	1.186
r_mcbond_it	0.636
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9282
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	163

Software

Software
Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.