2W42

THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT DNA DUPLEX.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.652.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.838α = 75.8
b = 61.384β = 75.86
c = 103.54γ = 79.47
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.832.7295.90.059.622.098992825.2
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)
11.9295.50.421.62.09

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 1W9H1.998.0689899446395.90.2070.2050.243RANDOM33.18
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]
-0.9980.0040.6041.433-0.516-0.478
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.156
r_dihedral_angle_4_deg20.451
r_dihedral_angle_3_deg16.316
r_dihedral_angle_1_deg6.233
r_scangle_it3.828
r_scbond_it2.624
r_mcangle_it1.987
r_angle_refined_deg1.766
r_mcbond_it1.241
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.156
r_dihedral_angle_4_deg20.451
r_dihedral_angle_3_deg16.316
r_dihedral_angle_1_deg6.233
r_scangle_it3.828
r_scbond_it2.624
r_mcangle_it1.987
r_angle_refined_deg1.766
r_mcbond_it1.241
r_nbtor_refined0.309
r_nbd_refined0.231
r_xyhbond_nbd_refined0.191
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.134
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6370
Nucleic Acid Atoms452
Solvent Atoms411
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing