3P6Z | pdb_00003p6z

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), 30 mM Ca2+, 30 mM Mg2+, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.208	α = 99.38
b = 62.259	β = 110.46
c = 67.51	γ = 92.26

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	ADSC QUANTUM 315r		2009-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9725	ESRF	ID23-1

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	1.69	62.14	94.2	0.08	12.3	3.3	86824	81788

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.696	1.79	89.6

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1PPB	1.7	31.92	81788	79739	2047	94.49	0.20059	0.20059	0.1996	0.2	0.23876	0.24	RANDOM	27.861

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]
			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.072
r_dihedral_angle_3_deg	16.216
r_dihedral_angle_4_deg	15.686
r_dihedral_angle_1_deg	7.349
r_scangle_it	4.81
r_scbond_it	3.166
r_mcangle_it	2.075
r_angle_refined_deg	2.032
r_mcbond_it	1.3
r_chiral_restr	0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.072
r_dihedral_angle_3_deg	16.216
r_dihedral_angle_4_deg	15.686
r_dihedral_angle_1_deg	7.349
r_scangle_it	4.81
r_scbond_it	3.166
r_mcangle_it	2.075
r_angle_refined_deg	2.032
r_mcbond_it	1.3
r_chiral_restr	0.15
r_bond_refined_d	0.023
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4733
Nucleic Acid Atoms
Solvent Atoms	505
Heterogen Atoms	108

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.