3Q4S

Crystal Structure of Human Glycogenin-1 (GYG1), apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LL3pdb id 1LL3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293.1520% PEG smears (PEG 2000, 3350, 4000, 5000MME), 0.1M PIPES, pH 7.0, 0.1M MgCl2, 0.1M KCl, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4249.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.02α = 90
b = 101.22β = 90
c = 48.75γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-12-04MSINGLE 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
11.9830.04970.09412.24.4199791995425.8
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)
11.982.0994.90.69924.42784

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 id 1LL31.9829.1721995418959101796.520.181460.178440.23827RANDOM23.295
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]
-0.59-1.412.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.693
r_dihedral_angle_4_deg20.208
r_dihedral_angle_3_deg13.344
r_dihedral_angle_1_deg5.929
r_scangle_it5.925
r_scbond_it4.356
r_mcangle_it2.676
r_mcbond_it1.716
r_angle_refined_deg1.462
r_angle_other_deg1.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.693
r_dihedral_angle_4_deg20.208
r_dihedral_angle_3_deg13.344
r_dihedral_angle_1_deg5.929
r_scangle_it5.925
r_scbond_it4.356
r_mcangle_it2.676
r_mcbond_it1.716
r_angle_refined_deg1.462
r_angle_other_deg1.013
r_mcbond_other0.461
r_chiral_restr0.092
r_bond_refined_d0.015
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 Atoms1981
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms37

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling