3GU6

Crystal structure of DAPKQ23V-ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82950.1 M Tris, 1.8 M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.935.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.87α = 90
b = 62.271β = 90
c = 88.114γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 300 mm CCDBe lenses2008-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

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
11.493099.4411.57.3423444234423.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.491.5594.33.86.92777

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 1JKS1.4929.36540155213099.440.184660.183140.21262RANDOM17.893
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]
-0.350.4-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.726
r_dihedral_angle_4_deg20.499
r_dihedral_angle_3_deg14.297
r_dihedral_angle_1_deg5.443
r_scangle_it3.446
r_scbond_it2.124
r_mcangle_it1.318
r_angle_refined_deg1.305
r_mcbond_it0.768
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.726
r_dihedral_angle_4_deg20.499
r_dihedral_angle_3_deg14.297
r_dihedral_angle_1_deg5.443
r_scangle_it3.446
r_scbond_it2.124
r_mcangle_it1.318
r_angle_refined_deg1.305
r_mcbond_it0.768
r_nbtor_refined0.308
r_xyhbond_nbd_refined0.223
r_nbd_refined0.21
r_symmetry_vdw_refined0.192
r_symmetry_hbond_refined0.15
r_chiral_restr0.089
r_bond_refined_d0.009
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2395
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms27

Software

Software
Software NamePurpose
BLU-MAXdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling