2F9D

2.5 angstrom resolution structure of the spliceosomal protein p14 bound to region of SF3b155


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629814-18% PEG3350, MOPS buffer, 0.2M sodium formate selenomethionine derivatized SF3b155 protein, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0359.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.87α = 90
b = 115.227β = 90
c = 82.536γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-08-25MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.10.979547, 1.019859ALS8.3.1

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
12.510099.50.07625.517097
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)
12.52.5995.60.3992.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.576.251622585899.560.224030.22140.27562RANDOM45.447
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]
-4.84.630.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.325
r_dihedral_angle_3_deg23.124
r_dihedral_angle_4_deg21.468
r_dihedral_angle_1_deg6.196
r_scangle_it2.718
r_scbond_it1.745
r_angle_refined_deg1.608
r_mcangle_it1.182
r_mcbond_it0.644
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.325
r_dihedral_angle_3_deg23.124
r_dihedral_angle_4_deg21.468
r_dihedral_angle_1_deg6.196
r_scangle_it2.718
r_scbond_it1.745
r_angle_refined_deg1.608
r_mcangle_it1.182
r_mcbond_it0.644
r_nbtor_refined0.314
r_nbd_refined0.225
r_symmetry_vdw_refined0.21
r_xyhbond_nbd_refined0.152
r_symmetry_hbond_refined0.147
r_chiral_restr0.134
r_bond_refined_d0.015
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 Atoms2560
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction