3ELA | pdb_00003ela

Crystal structure of active site inhibited coagulation factor VIIA mutant 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	100mM NaCitrate, 16%(w/v) PEG4000, 12%(v/v) 1-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.361	α = 90
b = 68.558	β = 90.22
c = 78.817	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	80	CCD				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.08	MAX II	I911-3

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	2.2	29.19	80.3	0.096		1.8	34658	34658			23.5

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	2.2	2.3	26.1		0.229	2.12	1.3	1526

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 (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	PDB ENTRY 1DAN	2.2	29.19	34719	32936	1734	100	0.23568	0.23259	0.24	0.2943	0.29	RANDOM	33.911

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]
-2.13		0.61	-2.32		4.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.327
r_dihedral_angle_4_deg	19.654
r_dihedral_angle_3_deg	18.403
r_dihedral_angle_1_deg	11.67
r_scangle_it	3.171
r_angle_refined_deg	2.17
r_scbond_it	2.124
r_mcangle_it	1.667
r_mcbond_it	0.958
r_symmetry_vdw_refined	0.526

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.327
r_dihedral_angle_4_deg	19.654
r_dihedral_angle_3_deg	18.403
r_dihedral_angle_1_deg	11.67
r_scangle_it	3.171
r_angle_refined_deg	2.17
r_scbond_it	2.124
r_mcangle_it	1.667
r_mcbond_it	0.958
r_symmetry_vdw_refined	0.526
r_nbtor_refined	0.319
r_symmetry_hbond_refined	0.308
r_nbd_refined	0.275
r_xyhbond_nbd_refined	0.219
r_metal_ion_refined	0.16
r_chiral_restr	0.134
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4119
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	56

Software

Software
Software Name	Purpose
MAR345	data collection
CCP4	model building
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CCP4	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.