3RMW

Crystal Structure of Human Glycogenin-1 (GYG1) T83M mutant complexed with manganese and UDP-glucose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293.1525% PEG smears (PEG 6k, 8k, 10k), 0.2M MgCl2, 10% glycerol, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.3647.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.65α = 90
b = 100.61β = 90
c = 49.1γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-10-26MSINGLE 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
11.9329.851000.09710.74.5218062180625.5
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)
11.932.031000.72824.43129

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 3Q4S1.9328.8622180620690111699.980.186740.18410.23735RANDOM22.627
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]
-0.61-0.541.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.602
r_dihedral_angle_4_deg16.575
r_dihedral_angle_3_deg13.224
r_dihedral_angle_1_deg6.947
r_sphericity_free5.476
r_sphericity_bonded5.33
r_scangle_it3.478
r_scbond_it2.292
r_mcangle_it1.464
r_angle_refined_deg1.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.602
r_dihedral_angle_4_deg16.575
r_dihedral_angle_3_deg13.224
r_dihedral_angle_1_deg6.947
r_sphericity_free5.476
r_sphericity_bonded5.33
r_scangle_it3.478
r_scbond_it2.292
r_mcangle_it1.464
r_angle_refined_deg1.404
r_mcbond_it0.84
r_angle_other_deg0.823
r_mcbond_other0.222
r_chiral_restr0.092
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1954
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms86

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling