X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XA6PDB entry 1XA6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729830% Jeffamine ED-2001, 0.1M HEPES pH 7.0, 0.1 M Adenosine-5-triphosphate disodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.5151.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.49α = 90
b = 92.49β = 90
c = 47.095γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2006-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.818.4398.20.0913.83.52106421064-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8690.40.771.11.91912

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 entry 1XA61.818.431995619956108298.020.189780.186710.25131RANDOM36.411
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]
-1.11-0.56-1.111.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.101
r_dihedral_angle_4_deg21.355
r_dihedral_angle_3_deg14.146
r_dihedral_angle_1_deg5.05
r_scangle_it4.938
r_scbond_it3.81
r_mcangle_it2.427
r_mcbond_it1.848
r_angle_refined_deg1.498
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.101
r_dihedral_angle_4_deg21.355
r_dihedral_angle_3_deg14.146
r_dihedral_angle_1_deg5.05
r_scangle_it4.938
r_scbond_it3.81
r_mcangle_it2.427
r_mcbond_it1.848
r_angle_refined_deg1.498
r_nbtor_refined0.304
r_nbd_refined0.224
r_symmetry_hbond_refined0.19
r_symmetry_vdw_refined0.165
r_xyhbond_nbd_refined0.142
r_chiral_restr0.104
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1582
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms

Software

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