3U2T

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.1522.5% PEG smears, 0.2M Li2(SO4), 0.05M ZnCl2, 0.1M Bis-Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.244.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.35α = 90
b = 101.06β = 90
c = 47.83γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-10-22MSINGLE 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
12.0538.299.70.104105183601833028.9
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)
12.052.1699.20.6522.14.92636

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 3Q4S2.0536.992183601741794099.580.201440.199020.25114RANDOM33.638
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]
-0.22-2.412.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.112
r_dihedral_angle_4_deg15.112
r_dihedral_angle_3_deg13.286
r_dihedral_angle_1_deg5.921
r_scangle_it2.495
r_scbond_it1.669
r_angle_refined_deg1.521
r_angle_other_deg1.058
r_mcangle_it1.011
r_mcbond_it0.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.112
r_dihedral_angle_4_deg15.112
r_dihedral_angle_3_deg13.286
r_dihedral_angle_1_deg5.921
r_scangle_it2.495
r_scbond_it1.669
r_angle_refined_deg1.521
r_angle_other_deg1.058
r_mcangle_it1.011
r_mcbond_it0.556
r_mcbond_other0.124
r_chiral_restr0.087
r_bond_refined_d0.015
r_bond_other_d0.004
r_gen_planes_refined0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2007
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms17

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling