4QBG

Crystal structure of a stable adenylate kinase variant AKlse4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MKG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529332% (w/v) polyethylene glycol 4000, 250mM MgCl2, 100mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2745.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.817α = 90
b = 71.02β = 95.13
c = 45.555γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.9795PAL/PLS7A (6B, 6C1)

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
11.3750974558844220
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.4295.1

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 REPLACEMENTTHROUGHOUT4MKG1.3749.324337341955226596.730.181280.179150.22029RANDOM26.268
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]
0.44-1.28-0.460.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.683
r_dihedral_angle_4_deg17.163
r_dihedral_angle_3_deg12.297
r_long_range_B_refined8.48
r_long_range_B_other8.372
r_dihedral_angle_1_deg5.54
r_scangle_other4.615
r_scbond_it3.07
r_scbond_other3.068
r_angle_refined_deg2.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.683
r_dihedral_angle_4_deg17.163
r_dihedral_angle_3_deg12.297
r_long_range_B_refined8.48
r_long_range_B_other8.372
r_dihedral_angle_1_deg5.54
r_scangle_other4.615
r_scbond_it3.07
r_scbond_other3.068
r_angle_refined_deg2.51
r_mcangle_other1.882
r_mcangle_it1.88
r_mcbond_it1.499
r_mcbond_other1.496
r_angle_other_deg1.357
r_chiral_restr0.151
r_bond_refined_d0.026
r_gen_planes_refined0.015
r_gen_planes_other0.008
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1706
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms59

Software

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