3DJS | pdb_00003djs

Crystal structure of transthyretin variant L58H at acidic pH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F41

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	295	32% PEG 2000, 0.1M NaAc, 0.2M Am2SO4 , pH 4.6, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.846	α = 90
b = 85.694	β = 90
c = 64.478	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 315		2006-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.979	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	1.8	64.42	99.4	0.103	16.4	6.7	23088	23088

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	1.8	1.9	100		0.342	5.3	7	3343

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	1F41	1.8	64.42	23052	23052	1184	99.28	0.20478	0.2041	0.2	0.21742	0.22	RANDOM	26.831

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]
-0.12			0.07		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.16
r_dihedral_angle_4_deg	19.148
r_dihedral_angle_3_deg	17.571
r_scangle_it	9.957
r_scbond_it	8.003
r_dihedral_angle_1_deg	5.69
r_mcangle_it	4.691
r_mcbond_it	3.179
r_angle_refined_deg	1.464
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.243
r_nbd_refined	0.238
r_xyhbond_nbd_refined	0.19
r_chiral_restr	0.097
r_symmetry_hbond_refined	0.094
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
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	1796
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms

Software

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