9ZNB | pdb_00009znb

Crystal Structure of a DARPin Fused to the 1TEL Crystallization Chaperone via a Direct Helical Fusion in a 3-Fold Crystal Form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7N2B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	294	1.0 M Magnesium sulfate hydrate, 0.1 M Sodium acetate trihydrate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.12	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.286	α = 90
b = 83.286	β = 90
c = 58.431	γ = 120

Symmetry
Space Group	P 65

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 EIGER2 XE 16M	Rh coated collimating mirrors, K-B focusing mirrors	2024-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979460	SSRL	BL12-2

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	1.771	41.64	90.37	0.1493	0.1531	0.0335	0.998	13.52	20.3		21254			31.01

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	1.771	1.835	64.57		6.504	6.676	1.49	0.34	0.54	19.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.771	41.64	1.34	20369	1079	90.37	0.1954	0.1942	0.195	0.2195	0.2186	39.76

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.8821
f_angle_d	0.9782
f_chiral_restr	0.0582
f_bond_d	0.0116
f_plane_restr	0.0055

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1778
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	10

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing