8JZA | pdb_00008jza

Crystal structure of single domain antibody kt75 of human Thyroglobulin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4W6Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	4M K-acetate, 0.1 M sodium HEPES pH 7.0, 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2	38.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.751	α = 90
b = 47.589	β = 90
c = 64.237	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MAR CCD 165 mm		2022-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.97777	RRCAT INDUS-2	PX-BL21

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	1.35	38.75	100	0.055	0.059	0.021	0.999	18	7.9		26851			12.8

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	1.35	1.37	100		0.916	0.981	0.349	0.764	2.4	7.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.35	38.239	26796	1319	99.989	0.133	0.1304	0.13	0.1744	0.17	22.737

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]
0.881			-0.44		-0.441

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.852
r_dihedral_angle_4_deg	19.117
r_dihedral_angle_3_deg	10.769
r_rigid_bond_restr	9.416
r_dihedral_angle_1_deg	6.795
r_scangle_it	6.079
r_scangle_other	6.075
r_lrange_it	5.598
r_lrange_other	5.486
r_mcangle_it	5.175
r_scbond_it	5.148
r_scbond_other	5.143
r_mcangle_other	5.104
r_mcbond_it	4.907
r_mcbond_other	4.72
r_angle_refined_deg	1.621
r_angle_other_deg	0.577
r_symmetry_nbd_refined	0.431
r_nbd_refined	0.386
r_symmetry_xyhbond_nbd_refined	0.31
r_symmetry_nbd_other	0.204
r_nbd_other	0.202
r_nbtor_refined	0.2
r_xyhbond_nbd_refined	0.159
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	978
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	13

Software

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