9H6L | pdb_00009h6l

Human B4GALNT1 in Complex with UDP

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
3.22	61.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.183	α = 90
b = 133.527	β = 94.83
c = 86.922	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	2.67	66.76	99.3	0.127	0.15	0.079	0.989	8	6.8		38565

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)
	2.67	2.79	94.2		1.107	1.363	0.784	0.477	1.1	5.6

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	2.674	66.76	38317	1897	99.023	0.193	0.1911	0.1911	0.2327	0.2328	79.968

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]
2.466		-0.642	0.389		-2.707

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.609
r_dihedral_angle_6_deg	14.397
r_lrange_it	13.401
r_dihedral_angle_2_deg	10.538
r_scangle_it	10.122
r_dihedral_angle_1_deg	6.956
r_mcangle_it	6.926
r_scbond_it	6.919
r_mcbond_it	4.686
r_angle_refined_deg	2.006
r_nbtor_refined	0.318
r_symmetry_nbd_refined	0.257
r_nbd_refined	0.213
r_symmetry_xyhbond_nbd_refined	0.141
r_chiral_restr	0.127
r_xyhbond_nbd_refined	0.126
r_ncsr_local_group_1	0.104
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7184
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	138

Software

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