3DK0

Crystal structure of transthyretin variant L55P at acidic pH

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	295	32% PEG 400, 0.05-0.2M CaCl2, 0.1M NaHepes , pH 4.6, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.632	α = 90
b = 84.78	β = 90
c = 65.415	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	ADSC QUANTUM 210		2006-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9340	ESRF	ID14-1

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	1.85	51.3	98.1	0.062	19.8	6.3	19735	19735

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	1.85	1.95	89.7		0.434	3.5	4.2	2554

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	1F41	1.87	42.37	19703	19703	1001	96.78	0.20768	0.20692	0.2225	RANDOM	29.867

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]
-0.52			-0.31		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.252
r_dihedral_angle_3_deg	16.475
r_dihedral_angle_4_deg	14.83
r_scangle_it	8.497
r_scbond_it	5.597
r_dihedral_angle_1_deg	5.033
r_mcangle_it	4.907
r_mcbond_it	3.165
r_angle_refined_deg	1.001
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.183
r_nbd_refined	0.181
r_xyhbond_nbd_refined	0.159
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1790
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing