7Q3I | pdb_00007q3i

Human Transthyretin expressed in Vibrio natriegens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		In-house E. coli TTR structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	291.15	11.6 mg/mL protein in PBS pH 7.4 mixed 1:1 with MgFormate 0.1 M, 24 % PEG1000.

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.439	α = 90
b = 62.896	β = 90
c = 85.593	γ = 90

Symmetry
Space Group	P 21 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2021-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.979499	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.55	50.683	99	0.045	0.048	0.019	1	21.7	11.5		33691			20.267

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	8.49	89.3		0.605	0.751	0.437	0.772	1.4	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	In-house E. coli TTR structure	1.55	50.683	33632	1666	98.848	0.184	0.1819	0.19	0.227	0.23	23.007

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]
1.95			-0.461		-1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.538
r_dihedral_angle_4_deg	14.417
r_dihedral_angle_3_deg	11.05
r_rigid_bond_restr	7.864
r_dihedral_angle_1_deg	6.152
r_angle_other_deg	2.53
r_lrange_it	2.383
r_lrange_other	2.277
r_scangle_it	2.265
r_scangle_other	2.261
r_scbond_other	2.176
r_scbond_it	2.174
r_angle_refined_deg	1.985
r_mcangle_it	1.858
r_mcangle_other	1.858
r_mcbond_it	1.706
r_mcbond_other	1.703
r_symmetry_nbd_refined	0.252
r_symmetry_nbd_other	0.218
r_symmetry_xyhbond_nbd_refined	0.188
r_nbd_refined	0.187
r_nbtor_refined	0.18
r_nbd_other	0.173
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.114
r_ncsr_local_group_1	0.112
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.061
r_bond_other_d	0.037
r_gen_planes_other	0.023
r_bond_refined_d	0.018
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1666
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms

Software

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