3RMV

Crystal Structure of Human Glycogenin-1 (GYG1) T83M mutant 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 DROP7.5293.1528% PEG smears (PEG 2k, 3350, 4k, 5kMME), 0.05M MgSO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.3547.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.68α = 90
b = 100.72β = 90
c = 48.72γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2010-10-30MSINGLE 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
11.8229.791000.06712.852574625702
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)
11.821.921000.73924.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 3Q4S1.8228.342570224391130999.980.184940.182830.22616RANDOM25.446
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]
-0.77-0.681.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.157
r_dihedral_angle_3_deg13.174
r_dihedral_angle_4_deg11.829
r_sphericity_bonded11.65
r_scangle_it6.867
r_dihedral_angle_1_deg6.407
r_scbond_it4.783
r_mcangle_it3.29
r_mcbond_it2.211
r_angle_refined_deg1.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.157
r_dihedral_angle_3_deg13.174
r_dihedral_angle_4_deg11.829
r_sphericity_bonded11.65
r_scangle_it6.867
r_dihedral_angle_1_deg6.407
r_scbond_it4.783
r_mcangle_it3.29
r_mcbond_it2.211
r_angle_refined_deg1.456
r_angle_other_deg0.943
r_mcbond_other0.651
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1956
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms35

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling