5PAU

Crystal Structure of Factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-2-[3-[(2-amino-2-oxoethyl)-methylsulfonylamino]phenyl]acetamide;2,2,2-trifluoroacetic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		inhouse model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.22	α = 90
b = 95.22	β = 90
c = 116.69	γ = 90

Symmetry
Space Group	P 41 21 2

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	MARMOSAIC 225 mm CCD		2008-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.55	47.61	98.6	0.091	0.102	0.997	8.69	4.71		77109		-3	27.763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.59	98.9		1.454	1.693	0.258	0.82

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	inhouse model	1.55	47.62	72307	3856	97.41	0.182	0.1808	0.204	RANDOM	25.033

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]
-0.18			-0.18		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.649
r_dihedral_angle_4_deg	18.758
r_dihedral_angle_3_deg	13.317
r_dihedral_angle_1_deg	6.219
r_mcangle_it	2.785
r_mcbond_it	1.711
r_mcbond_other	1.708
r_angle_refined_deg	1.477
r_angle_other_deg	0.927
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.649
r_dihedral_angle_4_deg	18.758
r_dihedral_angle_3_deg	13.317
r_dihedral_angle_1_deg	6.219
r_mcangle_it	2.785
r_mcbond_it	1.711
r_mcbond_other	1.708
r_angle_refined_deg	1.477
r_angle_other_deg	0.927
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2376
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	66

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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.