3U2U

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and maltotetraose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q4S	PDB ENTRY 3Q4S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293.15	2.0M Ammonium Sulphate, 0.2M Na/K tartrate, 0.1M Na Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.765	α = 79.36
b = 46.844	β = 88.45
c = 69.848	γ = 77.2

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 315	Kirkpatrick Baez bimorph mirror pair	2010-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.45	45.6	94.5	0.043	15.7	3.7	95225	95223			16.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53	91.6		0.425	2.8	3.5	13479

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3Q4S	1.45	41.2	2	95223	90447	4776	94.52	0.16533	0.16388	0.1933	RANDOM	23.031

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]
1.01	-1.04	0.27	0.2	0.68	-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.949
r_dihedral_angle_4_deg	13.856
r_dihedral_angle_3_deg	12.288
r_scangle_it	7.058
r_dihedral_angle_1_deg	6.106
r_scbond_it	4.962
r_mcangle_it	3.715
r_mcbond_it	2.315
r_angle_refined_deg	1.526
r_angle_other_deg	0.967

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.949
r_dihedral_angle_4_deg	13.856
r_dihedral_angle_3_deg	12.288
r_scangle_it	7.058
r_dihedral_angle_1_deg	6.106
r_scbond_it	4.962
r_mcangle_it	3.715
r_mcbond_it	2.315
r_angle_refined_deg	1.526
r_angle_other_deg	0.967
r_mcbond_other	0.674
r_chiral_restr	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4149
Nucleic Acid Atoms
Solvent Atoms	599
Heterogen Atoms	181

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.