3QVB

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


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 Ammonium sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.448.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.4α = 90
b = 100.97β = 90
c = 48.94γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-01-22MSINGLE 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
12.2629.9799.70.09310.73.9138951386238.7
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)
12.262.3899.10.60523.91970

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 3Q4S2.2629.032138621316869399.720.202010.199290.25588RANDOM27.926
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]
-0.39-1.231.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.429
r_dihedral_angle_4_deg22.815
r_dihedral_angle_3_deg13.704
r_dihedral_angle_1_deg6.45
r_scangle_it3.445
r_scbond_it2.194
r_angle_refined_deg1.487
r_mcangle_it1.402
r_angle_other_deg0.991
r_mcbond_it0.746
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.429
r_dihedral_angle_4_deg22.815
r_dihedral_angle_3_deg13.704
r_dihedral_angle_1_deg6.45
r_scangle_it3.445
r_scbond_it2.194
r_angle_refined_deg1.487
r_mcangle_it1.402
r_angle_other_deg0.991
r_mcbond_it0.746
r_mcbond_other0.15
r_chiral_restr0.087
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1972
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms46

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling