2A6T

Crystal structure of S.pombe mRNA decapping enzyme Dcp2p


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2293Na/K phosphate, PEG200, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.481α = 90
b = 56.481β = 90
c = 301.528γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9798ESRFID29

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
12.5201870022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.56

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.5151186351768295399.920.25490.249810.24760.28878RANDOM22.666
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]
2.81.42.8-4.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.408
r_scangle_it2.019
r_angle_refined_deg1.317
r_scbond_it1.233
r_mcangle_it0.867
r_angle_other_deg0.851
r_mcbond_it0.464
r_nbd_other0.222
r_nbd_refined0.217
r_xyhbond_nbd_refined0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.408
r_scangle_it2.019
r_angle_refined_deg1.317
r_scbond_it1.233
r_mcangle_it0.867
r_angle_other_deg0.851
r_mcbond_it0.464
r_nbd_other0.222
r_nbd_refined0.217
r_xyhbond_nbd_refined0.212
r_symmetry_hbond_refined0.206
r_symmetry_vdw_other0.203
r_symmetry_vdw_refined0.15
r_nbtor_other0.085
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms3334
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SHARPphasing