3T7O | pdb_00003t7o

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

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	6.5	293.15	2.0M Ammonium Sulphate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.415	α = 79.54
b = 46.59	β = 88.75
c = 69.904	γ = 75.83

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	IMAGE PLATE	RIGAKU RAXIS IV		2010-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.85	30.4	92.9	0.094	9.5	3.8	44258	44222			18.2

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	1.85	1.95	88.5		0.424	2.8	3.5	6135

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3Q4S	1.85	28.33	2	44222	42005	2217	92.84	0.19809	0.19506	0.199	0.25501	0.2635	RANDOM	24.652

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]
1.22	-1.66	0.83	0.28	0.99	-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.435
r_dihedral_angle_4_deg	17.5
r_dihedral_angle_3_deg	12.924
r_dihedral_angle_1_deg	6.257
r_scangle_it	2.746
r_scbond_it	1.916
r_angle_refined_deg	1.62
r_mcangle_it	1.09
r_angle_other_deg	1.074
r_mcbond_it	0.641

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.435
r_dihedral_angle_4_deg	17.5
r_dihedral_angle_3_deg	12.924
r_dihedral_angle_1_deg	6.257
r_scangle_it	2.746
r_scbond_it	1.916
r_angle_refined_deg	1.62
r_mcangle_it	1.09
r_angle_other_deg	1.074
r_mcbond_it	0.641
r_mcbond_other	0.186
r_chiral_restr	0.12
r_bond_refined_d	0.015
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	4169
Nucleic Acid Atoms
Solvent Atoms	522
Heterogen Atoms	162

Software

Software
Software Name	Purpose
CrystalClear	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.