3RMW

Crystal Structure of Human Glycogenin-1 (GYG1) T83M mutant complexed with manganese and UDP-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	8	293.15	25% PEG smears (PEG 6k, 8k, 10k), 0.2M MgCl2, 10% glycerol, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.65	α = 90
b = 100.61	β = 90
c = 49.1	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	RIGAKU RAXIS IV		2010-10-26	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	1.93	29.85	100	0.097	10.7	4.5	21806	21806			25.5

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	1.93	2.03	100		0.728	2	4.4	3129

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	1.93	28.86	2	21806	20690	1116	99.98	0.18674	0.1841	0.23735	RANDOM	22.627

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]
-0.61			-0.54		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.602
r_dihedral_angle_4_deg	16.575
r_dihedral_angle_3_deg	13.224
r_dihedral_angle_1_deg	6.947
r_sphericity_free	5.476
r_sphericity_bonded	5.33
r_scangle_it	3.478
r_scbond_it	2.292
r_mcangle_it	1.464
r_angle_refined_deg	1.404

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.602
r_dihedral_angle_4_deg	16.575
r_dihedral_angle_3_deg	13.224
r_dihedral_angle_1_deg	6.947
r_sphericity_free	5.476
r_sphericity_bonded	5.33
r_scangle_it	3.478
r_scbond_it	2.292
r_mcangle_it	1.464
r_angle_refined_deg	1.404
r_mcbond_it	0.84
r_angle_other_deg	0.823
r_mcbond_other	0.222
r_chiral_restr	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1954
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	86

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	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.