8Y9S | pdb_00008y9s

Crystal structure of nanobody MY6321 bound to human serum albumin (HSA)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N5U
experimental model	PDB	1E7A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.15 M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.26	α = 90
b = 143.9	β = 100.23
c = 93.67	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER X 16M		2023-01-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.979183	SSRF	BL10U2

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	2.88	46.25	99.4	0.286	0.31	0.12	0.983	5.5	6.6		38264

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	2.88	2.95		99.4	2.018	2.183	0.825	0.436		6.8

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 (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	2.88	46.25	36434	1808	99.27	0.23313	0.23008	0.253	0.29265	0.306	RANDOM	72.932

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]
6.6		2.23	-5.73		-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.284
r_long_range_B_other	15.589
r_long_range_B_refined	15.588
r_scangle_other	10.099
r_mcangle_it	9.976
r_mcangle_other	9.976
r_dihedral_angle_2_deg	8.568
r_dihedral_angle_1_deg	7.844
r_scbond_it	6.234
r_scbond_other	6.233
r_mcbond_it	6.228
r_mcbond_other	6.227
r_angle_refined_deg	1.545
r_angle_other_deg	0.556
r_chiral_restr	0.157
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10903
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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