5X6J

Crystal structure of B. globisporus adenylate kinase variant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S3G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2932.5M ammonium sulfate, 1% polyethylene glycol 1000, 0.1% Sodium azide, 50mM HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.4249.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.106α = 90
b = 65.106β = 90
c = 94.565γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2011-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.15099.853.9821.613990
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)
12.12.181000.50821.9

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 REPLACEMENTTHROUGHOUT1S3G2.1501314368398.790.196790.19310.27611RANDOM49.319
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]
-0.16-0.08-0.160.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.414
r_dihedral_angle_4_deg16.465
r_dihedral_angle_3_deg15.244
r_long_range_B_other7.313
r_long_range_B_refined7.312
r_dihedral_angle_1_deg6.077
r_scangle_other5.698
r_mcangle_it4.299
r_mcangle_other4.299
r_scbond_it3.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.414
r_dihedral_angle_4_deg16.465
r_dihedral_angle_3_deg15.244
r_long_range_B_other7.313
r_long_range_B_refined7.312
r_dihedral_angle_1_deg6.077
r_scangle_other5.698
r_mcangle_it4.299
r_mcangle_other4.299
r_scbond_it3.84
r_scbond_other3.838
r_mcbond_it3.244
r_mcbond_other3.235
r_angle_refined_deg2.043
r_angle_other_deg0.881
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1648
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing