2UYY

Structure of the cytokine-like nuclear factor n-pac


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VPDPDB ENTRY 1VPD, 2I9P
experimental modelPDB 2I9PPDB ENTRY 1VPD, 2I9P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG3350 0.20 M KSCN
Crystal Properties
Matthews coefficientSolvent content
3.261

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.18α = 90
b = 134.18β = 90
c = 261.463γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRRESEARCH2007-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.547.799.80.158.935.6160779
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)
12.52.5998.30.542.354.42

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1VPD, 2I9P2.5505762130721000.1720.170.211RANDOM29.62
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]
1.840.921.84-2.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.664
r_dihedral_angle_4_deg16.436
r_dihedral_angle_3_deg16.025
r_scangle_it11.457
r_scbond_it8.62
r_dihedral_angle_1_deg5.181
r_mcangle_it3.978
r_mcbond_it2.051
r_angle_refined_deg1.286
r_angle_other_deg0.885
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.664
r_dihedral_angle_4_deg16.436
r_dihedral_angle_3_deg16.025
r_scangle_it11.457
r_scbond_it8.62
r_dihedral_angle_1_deg5.181
r_mcangle_it3.978
r_mcbond_it2.051
r_angle_refined_deg1.286
r_angle_other_deg0.885
r_symmetry_vdw_other0.362
r_nbd_refined0.228
r_nbtor_refined0.184
r_nbd_other0.178
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.113
r_nbtor_other0.089
r_chiral_restr0.069
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8709
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing