5PB0 | pdb_00005pb0

Crystal Structure of Factor VIIa in complex with 2-(4-ethoxy-3-methoxyphenyl)-2-(isoquinolin-6-ylamino)acetic acid

X-RAY DIFFRACTION

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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 = 95.272	α = 90
b = 95.272	β = 90
c = 116.071	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	IMAGE PLATE	MAR scanner 345 mm plate		2007-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54178

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	1.98	50	98.7	0.1	9.6	11.4		37699

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	1.98	2.05	86.9		0.603		7.9	3250

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	1.98	49.57	34095	1795	94.73	0.1688	0.1675	0.18	0.1931	0.2	RANDOM	25.314

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]
-0.3			-0.3		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.623
r_dihedral_angle_4_deg	22.949
r_dihedral_angle_3_deg	15.021
r_dihedral_angle_1_deg	6.259
r_scangle_it	3.321
r_scbond_it	2.124
r_mcangle_it	1.546
r_angle_refined_deg	1.382
r_mcbond_it	1.068
r_angle_other_deg	0.919
r_symmetry_vdw_other	0.266
r_nbd_other	0.208
r_mcbond_other	0.207
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.174
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.166
r_metal_ion_refined	0.092
r_chiral_restr	0.09
r_nbtor_other	0.081
r_symmetry_vdw_refined	0.074
r_bond_refined_d	0.013
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	2363
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	61

Software

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