3U2V

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.152.0M Ammonium Sulphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4649.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.679α = 79.56
b = 46.739β = 88.71
c = 69.69γ = 76.86
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Q315 3x3 CCDKirkpatrick Baez bimorph mirror pair2010-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.545.4594.90.04311.42.48575385751
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)
11.51.5892.20.3622.42.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 3Q4S1.544.768575381446430694.920.182550.18070.21743RANDOM19.583
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]
0.55-0.840.360.290.59-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.062
r_dihedral_angle_3_deg11.768
r_dihedral_angle_4_deg10.471
r_dihedral_angle_1_deg5.852
r_angle_refined_deg1.514
r_angle_other_deg0.93
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.062
r_dihedral_angle_3_deg11.768
r_dihedral_angle_4_deg10.471
r_dihedral_angle_1_deg5.852
r_angle_refined_deg1.514
r_angle_other_deg0.93
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4150
Nucleic Acid Atoms
Solvent Atoms608
Heterogen Atoms242

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling