3T7N

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a monoclinic 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 DROP8.5293.1520% PEG 3350, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.244.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.02α = 90
b = 80.72β = 100.92
c = 69.85γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-01-19MSINGLE 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
11.9830.4397.30.07410.73.3347163469425.2
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)
11.982.0995.30.4972.13.24921

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 3Q4S1.9829.1623469432947174596.990.206320.203260.26546RANDOM34.106
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]
-1.43-2.482.61-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.521
r_dihedral_angle_4_deg18.51
r_dihedral_angle_3_deg15
r_dihedral_angle_1_deg6.395
r_scangle_it2.772
r_scbond_it1.947
r_angle_refined_deg1.487
r_mcangle_it1.234
r_angle_other_deg0.974
r_mcbond_it0.701
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.521
r_dihedral_angle_4_deg18.51
r_dihedral_angle_3_deg15
r_dihedral_angle_1_deg6.395
r_scangle_it2.772
r_scbond_it1.947
r_angle_refined_deg1.487
r_mcangle_it1.234
r_angle_other_deg0.974
r_mcbond_it0.701
r_mcbond_other0.17
r_chiral_restr0.089
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 Atoms4027
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms52

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling