4WZJ | pdb_00004wzj

Spliceosomal U4 snRNP core domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PJO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2934-10% PEG 550 MME, 0.1M KSCN or (NH4)2SO4, 0.1 M TRIS PH 8.0-8.5 10 MM MGCL2, 2 MM CYCLEN.
Crystal Properties
Matthews coefficientSolvent content
3.663

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 248.01α = 90
b = 248.01β = 90
c = 251.94γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.9795SRSPX9.6

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
13.5966.1682.90.213.32202467202467
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)
13.593.6820.80.731.11.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4PJO3.666.154166779825183.0750.1790.178990.17670.180.22380.18Random selection128.369
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]
-5.014-5.01410.028
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it35.898
r_dihedral_angle_2_deg31.885
r_mcangle_it21.402
r_scangle_it21.113
r_dihedral_angle_4_deg16.173
r_dihedral_angle_3_deg15.51
r_mcbond_it13.21
r_scbond_it12.979
r_dihedral_angle_1_deg7.491
r_angle_refined_deg1.399
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms54046
Nucleic Acid Atoms17436
Solvent Atoms3
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing