2PUQ

Crystal structure of active site inhibited coagulation factor VIIA in complex with soluble tissue factor

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	0.1 M sodium citrate, pH 5.6, 16.0 % (w/v) PEG 4000, 12 % (v/v) 1-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.312	α = 90
b = 68.827	β = 90.74
c = 78.732	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	100	CCD			2005-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.05	SLS	X06SA

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	2.05	39.15	99.6	0.132	8	4.2	52511	52511

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	2.05	2.1	98.9		0.69	2.26	4.1	3582

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DAN	2.05	39.15	52510	52510	2626	100	0.231	0.231	0.228	0.273	RANDOM	39.466

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]
-3.14		0.69	-1.45		4.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.609
r_dihedral_angle_3_deg	17.341
r_dihedral_angle_4_deg	16.084
r_dihedral_angle_1_deg	15.64
r_mcangle_it	3.894
r_scangle_it	3.719
r_mcbond_it	2.759
r_scbond_it	2.72
r_angle_refined_deg	2.495
r_nbtor_refined	0.338

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.609
r_dihedral_angle_3_deg	17.341
r_dihedral_angle_4_deg	16.084
r_dihedral_angle_1_deg	15.64
r_mcangle_it	3.894
r_scangle_it	3.719
r_mcbond_it	2.759
r_scbond_it	2.72
r_angle_refined_deg	2.495
r_nbtor_refined	0.338
r_nbd_refined	0.289
r_symmetry_vdw_refined	0.263
r_xyhbond_nbd_refined	0.262
r_symmetry_hbond_refined	0.208
r_chiral_restr	0.194
r_metal_ion_refined	0.055
r_bond_refined_d	0.028
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4097
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
PHASER	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.