3CFT | pdb_00003cft

Crystal structure of human transthyretin in complex with 1-amino-5-naphthalene sulfonate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.96	α = 90
b = 85.61	β = 90
c = 63.8	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	IMAGE PLATE	MAR scanner 345 mm plate	Osmic	2005-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU ULTRAX 18	1.5418

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	1.87	85.749	96.8	0.059	0.059	9.7	4.1	20234	19759	2	2	23.6

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)
	1.87	1.96	83.1		0.457	0.457	1.6	4	2423

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 (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 3CFM	1.87	38.4	20234	19755	1017	98.36	0.194	0.194	0.191	0.1881	0.239	0.2356	RANDOM	25.477

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]
0.02			-0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.837
r_dihedral_angle_4_deg	21.345
r_dihedral_angle_3_deg	16.262
r_dihedral_angle_1_deg	6.741
r_scangle_it	4.556
r_scbond_it	2.948
r_mcangle_it	1.963
r_angle_refined_deg	1.664
r_mcbond_it	1.229
r_symmetry_hbond_refined	0.361
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.225
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.185
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1929
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	45

Software

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