Experiment: 3DGV

Crystal structure of thrombin activatable fibrinolysis inhibitor (TAFI)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	296	Protein solution: 8 mg/ml protein in 20 mM Tris-HCl, 120 mM NaCl at pH 7.4. reservoir solution: 100 mM Tris-HCl pH 8.0, 1.5 M ammonium sulfate, 2% benzamidine. 10 ul sodium malonate was added to the reservoir the next day after setting up the drop., VAPOR DIFFUSION, Hanging drop, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
4.45	72.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.47	α = 90
b = 146.47	β = 90
c = 231.69	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	ADSC QUANTUM 4		2005-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.933	ESRF	ID14-3

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	2.5	90	99.2	0.122	29.2	32.2	87561	86894			54.4

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	2.5	2.6	95.4		0.913	4.8	30.4	9108

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1NSA	2.5	19.86	86892	4345	99.2	0.205	0.2082	0.243	0.2442	72.26

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]
6.549			6.549		-13.098

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	1.755
c_mcangle_it	1.508
c_scbond_it	1.047
c_angle_d	0.887
c_mcbond_it	0.832
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9621
Nucleic Acid Atoms
Solvent Atoms	1019
Heterogen Atoms	375

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling