3D66

Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	277	16-18% PEG 3000, 0.18-0.22mM Na/K-tartrate, 50mM L-glutamate, 50 mM L-arginine, pH 6.0, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.74	α = 90
b = 161.74	β = 90
c = 139.45	γ = 120

Symmetry
Space Group	P 31 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	ADSC QUANTUM 315		2007-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.26206	ESRF	ID29

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	3.1	49.51	100	0.105	13.9	8.6	38621	38593		-3.7

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	3.1	3.27	100		0.833	2.6	8.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1KWM	3.1	49.51	36638	36638	1953	99.99	0.20621	0.20442	0.24038	RANDOM	80.939

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]
3.98	1.99		3.98		-5.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.063
r_dihedral_angle_3_deg	17.734
r_dihedral_angle_4_deg	17.174
r_dihedral_angle_1_deg	10.449
r_scangle_it	2.369
r_angle_refined_deg	1.751
r_scbond_it	1.58
r_mcangle_it	1.198
r_angle_other_deg	1.099
r_mcbond_it	0.959
r_symmetry_vdw_other	0.342
r_symmetry_vdw_refined	0.31
r_nbd_refined	0.246
r_symmetry_hbond_refined	0.225
r_nbd_other	0.21
r_xyhbond_nbd_refined	0.208
r_nbtor_refined	0.204
r_mcbond_other	0.126
r_xyhbond_nbd_other	0.102
r_chiral_restr	0.098
r_nbtor_other	0.094
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.003
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9735
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	129

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
SCALA	data scaling
PHASER	phasing