9H6K | pdb_00009h6k

Human B4GALNT1 in Complex with UDP-GalNac

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M Tris-BICINE, 30% w/v GOL_P4K (40% v/v Glycerol, 20% w/v PEG 4000), 0.2 M Sodium formate, 0.2 M Ammonium acetate, 0.2 M Sodium citrate tribasic dihydrate, 0.2 M Potassium sodium tartrate tetrahydrate, 0.2 M Sodium oxamate

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.1	α = 90
b = 134.922	β = 95.907
c = 86.584	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 EIGER2 X CdTe 9M		2024-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.6199	Diamond	I24

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	2.75	54.66	99.5	0.186	0.219	0.114	0.992	6.2	7		35584

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)
	2.75	2.88	96.3		1.442	1.742	0.964	0.389	1	6.3

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	2.75	54.656	35558	1761	99.602	0.19	0.1887	0.1887	0.2248	0.2248	75.617

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]
0.834		-0.836	-0.845		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.28
r_dihedral_angle_6_deg	14.932
r_lrange_it	13.35
r_dihedral_angle_2_deg	10.629
r_scangle_it	9.529
r_mcangle_it	7.115
r_dihedral_angle_1_deg	6.838
r_scbond_it	6.331
r_mcbond_it	4.606
r_angle_refined_deg	1.884
r_symmetry_xyhbond_nbd_refined	0.323
r_nbtor_refined	0.309
r_symmetry_nbd_refined	0.296
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.123
r_ncsr_local_group_1	0.091
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7316
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	200

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data collection
Aimless	data scaling
PHASER	phasing
ISOLDE	model building
Coot	model building
DIALS	data reduction