4IK7 | pdb_00004ik7

Crystal structure of human transthyretin in complex with indomethacin

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.2M Calcium chloride, 0.1M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.03	α = 90
b = 83.57	β = 90
c = 63.06	γ = 90

Symmetry
Space Group	P 21 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	MARMOSAIC 325 mm CCD		2008-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.42500	LNLS	D03B-MX1

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	2.1	83.624	99.9	0.085	0.085	12	3.4	13519	13519

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	99.9		0.377	0.377	0.448	0.238	1.9	3.4	1918

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.1	21.79	13517	667	99.96	0.2039	0.2019	0.2002	0.2436	0.2425	RANDOM	27.7372

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]
0.24			-0.09		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.034
r_dihedral_angle_4_deg	16.95
r_dihedral_angle_3_deg	15.88
r_dihedral_angle_1_deg	5.863
r_angle_refined_deg	1.37
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.304
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.139
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1785
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	50

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
REFMAC	phasing