3FB4

Crystal structure of adenylate kinase from Marinibacillus marinus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S3GPDB ID 1S3G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52830.5 % LDAO,150 mM sodium chloride 1.5 M tri-Sodium citrate, 9mM p1,p5-Di(adenosine-5')pentaphosphate pentasodium salt, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.7755.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.639α = 90
b = 46.506β = 98.67
c = 62.669γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATERIGAKU RAXIS IVRigaku Osmic Mirrors2008-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54

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
1233.4298.70.029242.8118017177863
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)
22.0796.90.089.42.46

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 REPLACEMENTTHROUGHOUTPDB ID 1S3G220177861689590198.860.182750.180430.22606RANDOM19.117
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]
0.32-0.34-0.50.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.374
r_dihedral_angle_3_deg18.026
r_dihedral_angle_4_deg11.364
r_dihedral_angle_1_deg5.721
r_scangle_it5.007
r_scbond_it3.04
r_angle_refined_deg1.931
r_mcangle_it1.737
r_mcbond_it0.885
r_chiral_restr0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.374
r_dihedral_angle_3_deg18.026
r_dihedral_angle_4_deg11.364
r_dihedral_angle_1_deg5.721
r_scangle_it5.007
r_scbond_it3.04
r_angle_refined_deg1.931
r_mcangle_it1.737
r_mcbond_it0.885
r_chiral_restr0.133
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1674
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms58

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling