2BFW

Structure of the C domain of glycogen synthase from Pyrococcus abyssi


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RZUPDB ENTRY 1RZU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.630% PEG8K, 0.1 M NAAC PH 4.5, 0.2M LITHIUM SULPHATE
Crystal Properties
Matthews coefficientSolvent content
1.936.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.614α = 90
b = 50.82β = 106.89
c = 44.261γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEAERCHFLAT MIRROR AND A TOROIDAL MIRROR2004-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM16ESRFBM16

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
11.837.997.60.0515.22.4157012
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)
11.81.985.90.253.52

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1RZU1.842.331458174497.60.1860.1830.235RANDOM15.64
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]
-0.36-0.090.070.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.745
r_dihedral_angle_4_deg16.642
r_dihedral_angle_3_deg14.337
r_dihedral_angle_1_deg5.172
r_scangle_it2.237
r_scbond_it1.396
r_angle_refined_deg0.989
r_mcangle_it0.914
r_mcbond_it0.812
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.745
r_dihedral_angle_4_deg16.642
r_dihedral_angle_3_deg14.337
r_dihedral_angle_1_deg5.172
r_scangle_it2.237
r_scbond_it1.396
r_angle_refined_deg0.989
r_mcangle_it0.914
r_mcbond_it0.812
r_nbtor_refined0.301
r_symmetry_vdw_refined0.206
r_nbd_refined0.195
r_symmetry_hbond_refined0.121
r_xyhbond_nbd_refined0.111
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1532
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing