5PB3

Crystal Structure of Factor VIIa in complex with 1-[[3-[4-(5-amino-1H-pyrrolo[3,2-b]pyridin-2-yl)-5-hydroxypyrazol-1-yl]phenyl]methyl]-3-phenylurea

X-RAY DIFFRACTION

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
3.75	67.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.192	α = 90
b = 95.192	β = 90
c = 116.08	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		2008-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.98399	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	49.56	98.6	0.124	0.124	10.71	8.69		42139

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	90.9		0.493	0.493	1.89	3.13

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	1.9	47.62	39463	2091	97.42	0.1921	0.1911	0.2112	RANDOM	23.534

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]
-0.46			-0.46		0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.471
r_dihedral_angle_4_deg	17.653
r_dihedral_angle_3_deg	14.375
r_dihedral_angle_1_deg	5.863
r_angle_other_deg	2.636
r_scangle_it	2.259
r_angle_refined_deg	1.482
r_scbond_it	1.309
r_mcangle_it	1.128
r_mcbond_it	0.603

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.471
r_dihedral_angle_4_deg	17.653
r_dihedral_angle_3_deg	14.375
r_dihedral_angle_1_deg	5.863
r_angle_other_deg	2.636
r_scangle_it	2.259
r_angle_refined_deg	1.482
r_scbond_it	1.309
r_mcangle_it	1.128
r_mcbond_it	0.603
r_mcbond_other	0.079
r_chiral_restr	0.066
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2376
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SADABS	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.