3T7M

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a triclinic closed form


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, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.550.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.006α = 87.89
b = 47.081β = 78.88
c = 70.02γ = 76.65
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-12-22MSINGLE 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
11.845.8192.90.07712.33.8493404933519.5
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)
11.81.987.90.5242.33.46820

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 3Q4S1.838.2624933546827250892.870.191970.189230.24253RANDOM17.279
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]
0.63-1.180.660.630.26-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.568
r_dihedral_angle_3_deg13.681
r_dihedral_angle_4_deg12.854
r_dihedral_angle_1_deg6.352
r_angle_refined_deg1.552
r_angle_other_deg0.983
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.568
r_dihedral_angle_3_deg13.681
r_dihedral_angle_4_deg12.854
r_dihedral_angle_1_deg6.352
r_angle_refined_deg1.552
r_angle_other_deg0.983
r_chiral_restr0.092
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 Atoms4150
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms144

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling