2PY9

Protein-RNA Interaction involving KH1 domain from Human Poly(C)-Binding Protein-2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.129525% PEG 8000, 100mM sodium acetate, 100mM sodium cacodylate pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4148.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.006α = 90
b = 58.697β = 90
c = 71.496γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210KOHZU: Double Crystal Si(111)2005-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11588ALS8.3.1

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
12.5670.194.20.1020.09614.410.4123781166022
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)
2.562.62690.730.93.19.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.5640221165659194.210.220380.217980.26862RANDOM38.229
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]
-1.61-0.131.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.4
r_dihedral_angle_4_deg27.656
r_dihedral_angle_3_deg24.3
r_dihedral_angle_1_deg8.475
r_scangle_it5.004
r_scbond_it3.42
r_angle_refined_deg3.306
r_mcangle_it2.139
r_mcbond_it1.553
r_nbtor_refined0.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.4
r_dihedral_angle_4_deg27.656
r_dihedral_angle_3_deg24.3
r_dihedral_angle_1_deg8.475
r_scangle_it5.004
r_scbond_it3.42
r_angle_refined_deg3.306
r_mcangle_it2.139
r_mcbond_it1.553
r_nbtor_refined0.338
r_symmetry_vdw_refined0.321
r_nbd_refined0.286
r_xyhbond_nbd_refined0.173
r_chiral_restr0.155
r_symmetry_hbond_refined0.14
r_bond_refined_d0.032
r_gen_planes_refined0.011
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 Atoms2132
Nucleic Acid Atoms490
Solvent Atoms51
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing