4PKD

U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1URN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.229340% MPD, 0.15 M sodium chloride, 0.1 M sodium acetate, pH 4.2
Crystal Properties
Matthews coefficientSolvent content
2.3453

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.22α = 90
b = 66.6β = 110.95
c = 93.73γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I031.0332DiamondI03

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
12.587.5499.10.0760.047113.71611515967
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)
12.52.6499.40.353.23.7

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 REPLACEMENTTHROUGHOUT1URN2.5871515681299.070.199920.196750.25791RANDOM50.252
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]
3.18-0.120.23-2.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.277
r_dihedral_angle_4_deg19.822
r_dihedral_angle_3_deg19.723
r_long_range_B_refined8.964
r_long_range_B_other8.963
r_dihedral_angle_1_deg6.87
r_scangle_other5.608
r_mcangle_it4.168
r_mcangle_other4.166
r_scbond_it3.636
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.277
r_dihedral_angle_4_deg19.822
r_dihedral_angle_3_deg19.723
r_long_range_B_refined8.964
r_long_range_B_other8.963
r_dihedral_angle_1_deg6.87
r_scangle_other5.608
r_mcangle_it4.168
r_mcangle_other4.166
r_scbond_it3.636
r_scbond_other3.635
r_angle_other_deg3.142
r_mcbond_it2.735
r_mcbond_other2.735
r_angle_refined_deg1.91
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.014
r_bond_other_d0.013
r_gen_planes_other0.008
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1954
Nucleic Acid Atoms1177
Solvent Atoms113
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement