3FRO

Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BISPDB ENTRY 2BIS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429326-30% MPD, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8356.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.998α = 90
b = 139.913β = 90
c = 159.414γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.52599.70.0780.0998.43.958723583642255.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6497.60.410.321.13.71964

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTPDB ENTRY 2BIS2.524.9125852758364295099.390.2880.2160.2140.255RANDOM43.416
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]
-0.260.92-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.785
r_dihedral_angle_3_deg14.931
r_dihedral_angle_4_deg13.818
r_dihedral_angle_1_deg4.803
r_angle_refined_deg0.825
r_angle_other_deg0.74
r_scangle_it0.494
r_scbond_it0.322
r_mcangle_it0.245
r_mcbond_it0.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.785
r_dihedral_angle_3_deg14.931
r_dihedral_angle_4_deg13.818
r_dihedral_angle_1_deg4.803
r_angle_refined_deg0.825
r_angle_other_deg0.74
r_scangle_it0.494
r_scbond_it0.322
r_mcangle_it0.245
r_mcbond_it0.223
r_nbtor_refined0.173
r_nbd_other0.168
r_nbd_refined0.166
r_symmetry_vdw_other0.124
r_symmetry_vdw_refined0.113
r_symmetry_hbond_refined0.101
r_xyhbond_nbd_refined0.097
r_nbtor_other0.08
r_chiral_restr0.05
r_mcbond_other0.021
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10452
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing