7UT3 | pdb_00007ut3

Crystal structure of complex of Fab, G10C with GalNAc-pNP

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Z7X	6z7x, 1sy6
experimental model	PDB	1SY6	6z7x, 1sy6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	1.5M Ammonium Phosphate

Crystal Properties
Matthews coefficient	Solvent content
4.57	73.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.594	α = 90
b = 132.594	β = 90
c = 169.054	γ = 120

Symmetry
Space Group	P 61 2 2

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		2022-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	3	50	99.8	0.079	23.1	7.8		18216

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.05	99.1		1.8

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-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	6z7x, 1sy6	3	47.54	14099	587	80.62	0.1884	0.1861	0.1868	0.24	0.2311	RANDOM	89.477

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]
-0.45	-0.22		-0.45		1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.597
r_dihedral_angle_3_deg	21.628
r_dihedral_angle_4_deg	17.075
r_dihedral_angle_1_deg	8.201
r_rigid_bond_restr	6.547
r_angle_refined_deg	1.344
r_angle_other_deg	1.094
r_chiral_restr	0.049
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3276
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing