2OZB

Structure of a human Prp31-15.5K-U4 snRNA complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M calcium acetate, 0.1 M HEPES-NaOH, pH 7.0, 6 % PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3162.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.555α = 90
b = 99.896β = 90
c = 169.645γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2006-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.63099.70.1070.07613.710.8421554202911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.797.60.6630.6631.52.9

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 REPLACEMENTTHROUGHOUT1E7K2.6304215542029222799.670.207840.205690.24756RANDOM53.782
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]
0.990.35-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.293
r_dihedral_angle_3_deg20.839
r_dihedral_angle_4_deg20.115
r_dihedral_angle_1_deg5.411
r_scangle_it2.622
r_scbond_it1.563
r_angle_refined_deg1.501
r_mcangle_it1.19
r_mcbond_it0.661
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.293
r_dihedral_angle_3_deg20.839
r_dihedral_angle_4_deg20.115
r_dihedral_angle_1_deg5.411
r_scangle_it2.622
r_scbond_it1.563
r_angle_refined_deg1.501
r_mcangle_it1.19
r_mcbond_it0.661
r_nbtor_refined0.305
r_nbd_refined0.217
r_symmetry_vdw_refined0.204
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.138
r_chiral_restr0.1
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_metal_ion_refined0.003
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_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 Atoms5707
Nucleic Acid Atoms1406
Solvent Atoms228
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling