3T7O

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q4SPDB ENTRY 3Q4S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.152.0M Ammonium Sulphate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4349.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.415α = 79.54
b = 46.59β = 88.75
c = 69.904γ = 75.83
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8530.492.90.0949.53.8442584422218.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9588.50.4242.83.56135

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3Q4S1.8528.3324422242005221792.840.198090.195060.25501RANDOM24.652
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]
1.22-1.660.830.280.99-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.435
r_dihedral_angle_4_deg17.5
r_dihedral_angle_3_deg12.924
r_dihedral_angle_1_deg6.257
r_scangle_it2.746
r_scbond_it1.916
r_angle_refined_deg1.62
r_mcangle_it1.09
r_angle_other_deg1.074
r_mcbond_it0.641
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.435
r_dihedral_angle_4_deg17.5
r_dihedral_angle_3_deg12.924
r_dihedral_angle_1_deg6.257
r_scangle_it2.746
r_scbond_it1.916
r_angle_refined_deg1.62
r_mcangle_it1.09
r_angle_other_deg1.074
r_mcbond_it0.641
r_mcbond_other0.186
r_chiral_restr0.12
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4169
Nucleic Acid Atoms
Solvent Atoms522
Heterogen Atoms162

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling