5PAY | pdb_00005pay

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

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
3.76	67.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.1	α = 90
b = 95.1	β = 90
c = 116.49	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		2008-02-25	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	1.66	49.67	99.8	0.062	0.069	0.999	14.82	5.54		63461		-3	26.881

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	1.66	1.7	99.5		0.648	0.72	0.798	2.39

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	inhouse model	1.66	49.69	59528	3156	98.04	0.1826	0.182	0.19	0.1943	0.2	RANDOM	20.014

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]
-0.42			-0.42		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.077
r_dihedral_angle_4_deg	17.878
r_dihedral_angle_3_deg	14.418
r_dihedral_angle_1_deg	6.285
r_scangle_it	3.03
r_angle_other_deg	2.68
r_scbond_it	1.869
r_angle_refined_deg	1.57
r_mcangle_it	1.453
r_mcbond_it	0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.077
r_dihedral_angle_4_deg	17.878
r_dihedral_angle_3_deg	14.418
r_dihedral_angle_1_deg	6.285
r_scangle_it	3.03
r_angle_other_deg	2.68
r_scbond_it	1.869
r_angle_refined_deg	1.57
r_mcangle_it	1.453
r_mcbond_it	0.79
r_mcbond_other	0.15
r_chiral_restr	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2372
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	69

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.