3D67 | pdb_00003d67

Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI) in complex with 2-guanidino-ethyl-mercaptosuccinic acid (GEMSA)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D66	pdb entry 3D66

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, 50mM L-arginine, 1mM GEMSA, pH 6.0, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.05	α = 90
b = 161.05	β = 90
c = 138.99	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 315r		2007-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97320	ESRF	ID23-1

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	3.4	49.27	99.6	0.091	11.4	4.9	28920	28900		-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	3.4	3.58	100		0.63	2.2	5

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 3D66	3.4	44.09	27424	27424	1472	99.57	0.20043	0.19772	0.19	0.25218	0.25	RANDOM	100.733

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]
4.12	2.06		4.12		-6.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.753
r_dihedral_angle_3_deg	20.197
r_dihedral_angle_4_deg	17.8
r_dihedral_angle_1_deg	8.742
r_angle_refined_deg	1.485
r_scangle_it	1.407
r_angle_other_deg	0.945
r_scbond_it	0.872
r_mcangle_it	0.836
r_mcbond_it	0.471
r_metal_ion_refined	0.353
r_nbd_refined	0.237
r_symmetry_vdw_other	0.207
r_nbtor_refined	0.201
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.175
r_symmetry_vdw_refined	0.168
r_nbtor_other	0.096
r_symmetry_hbond_refined	0.092
r_chiral_restr	0.086
r_mcbond_other	0.059
r_xyhbond_nbd_other	0.017
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.003
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	9738
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	202

Software

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