3U2U

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293.152.0M Ammonium Sulphate, 0.2M Na/K tartrate, 0.1M Na Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4850.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.765α = 79.36
b = 46.844β = 88.45
c = 69.848γ = 77.2
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Kirkpatrick Baez bimorph mirror pair2010-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.4545.694.50.04315.73.7952259522316.7
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)
11.451.5391.60.4252.83.513479

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 3Q4S1.4541.229522390447477694.520.165330.163880.1933RANDOM23.031
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]
1.01-1.040.270.20.68-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.949
r_dihedral_angle_4_deg13.856
r_dihedral_angle_3_deg12.288
r_scangle_it7.058
r_dihedral_angle_1_deg6.106
r_scbond_it4.962
r_mcangle_it3.715
r_mcbond_it2.315
r_angle_refined_deg1.526
r_angle_other_deg0.967
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.949
r_dihedral_angle_4_deg13.856
r_dihedral_angle_3_deg12.288
r_scangle_it7.058
r_dihedral_angle_1_deg6.106
r_scbond_it4.962
r_mcangle_it3.715
r_mcbond_it2.315
r_angle_refined_deg1.526
r_angle_other_deg0.967
r_mcbond_other0.674
r_chiral_restr0.095
r_bond_refined_d0.016
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 Atoms4149
Nucleic Acid Atoms
Solvent Atoms599
Heterogen Atoms181

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling