3U2W

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and glucose or a glucal species


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293.1525% PEG 3350, 0.2M Li2(SO4), 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.1943.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.29α = 90
b = 80.18β = 100.67
c = 69.53γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-05-24MSINGLE 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
11.6822.781000.05513.94581195807022.6
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)
11.681.771000.5462.13.88458

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 3Q4S1.6822.58525811955123294699.910.158760.157050.19041RANDOM18.672
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]
-0.82-0.721.43-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.656
r_dihedral_angle_4_deg12.248
r_dihedral_angle_3_deg11.885
r_dihedral_angle_1_deg6.134
r_angle_refined_deg1.499
r_angle_other_deg0.974
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_deg35.656
r_dihedral_angle_4_deg12.248
r_dihedral_angle_3_deg11.885
r_dihedral_angle_1_deg6.134
r_angle_refined_deg1.499
r_angle_other_deg0.974
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 Atoms4067
Nucleic Acid Atoms
Solvent Atoms504
Heterogen Atoms105

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling