5X6I

Crystal structure of B. subtilis adenylate kinase variant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P3J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29340mM chloride, 36% polyethylene glycol 1500, 50mM CHES pH 9.0
Crystal Properties
Matthews coefficientSolvent content
2.0138.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.739α = 90
b = 44.18β = 90
c = 100.595γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDDECTRIS PILATUS 2M2012-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A0.96400Photon FactoryBL-1A

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
125099.929.084.713718
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)
122.031000.584.7

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 REPLACEMENTTHROUGHOUT1P3J2501299367999.550.183030.179230.25881RANDOM43.434
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]
0.94-2.21.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.976
r_dihedral_angle_3_deg14.28
r_dihedral_angle_4_deg12.364
r_long_range_B_refined7.584
r_long_range_B_other7.574
r_dihedral_angle_1_deg6.195
r_scangle_other5.56
r_mcangle_it3.899
r_mcangle_other3.898
r_scbond_it3.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.976
r_dihedral_angle_3_deg14.28
r_dihedral_angle_4_deg12.364
r_long_range_B_refined7.584
r_long_range_B_other7.574
r_dihedral_angle_1_deg6.195
r_scangle_other5.56
r_mcangle_it3.899
r_mcangle_other3.898
r_scbond_it3.615
r_scbond_other3.613
r_mcbond_it2.719
r_mcbond_other2.716
r_angle_refined_deg1.874
r_angle_other_deg0.89
r_chiral_restr0.091
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1654
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms61

Software

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