3D4U

Bovine thrombin-activatable fibrinolysis inhibitor (TAFIa) in complex with tick-derived carboxypeptidase inhibitor.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZLI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	0.2M (NH4)2SO4, 0.1M NaAcO, 10% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.2	α = 90
b = 84.2	β = 90
c = 127.9	γ = 120

Symmetry
Space Group	P 32 2 1

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	MAR CCD 165 mm	horizontally diffracting Si (111) monochromator and Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry as the focusing system.	2007-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

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	1.7	48.1	93.3	0.099	0.099	20.6	15.1	62124	57962			18.6

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	1.7	1.79	95.5		0.611	0.611	9.2	9.2	8032

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ZLI	1.7	48.08	62124	57265	695	99.34	0.15606	0.15606	0.15588	0.17071	RANDOM	20.858

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]
0.04	0.02		0.04		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.796
r_dihedral_angle_4_deg	15.732
r_dihedral_angle_3_deg	13.473
r_dihedral_angle_1_deg	5.646
r_scangle_it	3.663
r_scbond_it	2.302
r_mcangle_it	1.462
r_angle_refined_deg	1.345
r_mcbond_it	0.96
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.796
r_dihedral_angle_4_deg	15.732
r_dihedral_angle_3_deg	13.473
r_dihedral_angle_1_deg	5.646
r_scangle_it	3.663
r_scbond_it	2.302
r_mcangle_it	1.462
r_angle_refined_deg	1.345
r_mcbond_it	0.96
r_nbtor_refined	0.31
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.196
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.107
r_bond_refined_d	0.015
r_metal_ion_refined	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2968
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	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 R01GM133198.