8FPA | pdb_00008fpa

Structure of a chimeric antibody (Fab) fragment bound to de-N-acetyl polysialic acid (dPSA)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel		The search model was obtained by homology modeling (Swiss-Model) using the coordinates from PDB entry 6pe7 and the sequence of the Fab that was in this crystal.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	24% polyethylene glycol 1,500; 20% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.585	α = 90
b = 71.437	β = 92.954
c = 91.495	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 PILATUS3 S 6M		2021-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.0	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.83	74.49	99.9	0.081	0.999	9.1	6.8		84628			33.59

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.86	99.9		0.364	0.8	6.8

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6pe7	1.83	74.49	84628	1458	99.84	0.1856	0.1854	0.2297	0.2308	39.29

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]
2.90316975		-2.27503165	-1.75152163		-1.15164812

RMS Deviations
Key	Refinement Restraint Deviation
s_dihedral_angle_6_deg	15.3184
s_dihedral_angle_3_deg	10.6468
s_dihedral_angle_1_deg	7.3934
s_dihedral_angle_2_deg	6.4542
s_angle_nonh_deg	2.0623
s_nbtor	0.2259
s_nbd	0.2136
s_symmetry_nbd	0.1907
s_symmetry_hbond_nbd	0.1733
s_hbond_nbd	0.1482
s_chiral_restr	0.0893
s_bond_nonh_d	0.0124
s_planes	0.0103

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6567
Nucleic Acid Atoms
Solvent Atoms	407
Heterogen Atoms	263

Software

Software
Software Name	Purpose
Servalcat	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing