X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NPU1npu, 1pkq
experimental modelPDB 1PKQ1npu, 1pkq

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Sitting drop8.529120% PEG 6000, 0.1 M Tris pH 8.5, Sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5551.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.933α = 90
b = 84.056β = 107.88
c = 52.108γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9792NSLSX29A

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
11.73099.20.0789.84.639403
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)
11.71.7697.80.5733.5

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 REPLACEMENTTHROUGHOUT1npu, 1pkq1.824.953937831433166698.620.191690.18970.22848RANDOM29.223
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]
-0.280.341.34-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.161
r_dihedral_angle_4_deg20.965
r_dihedral_angle_3_deg15.806
r_dihedral_angle_1_deg11.976
r_scangle_it4.652
r_mcangle_it4.287
r_scbond_it3.234
r_mcbond_it2.987
r_angle_refined_deg1.347
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.161
r_dihedral_angle_4_deg20.965
r_dihedral_angle_3_deg15.806
r_dihedral_angle_1_deg11.976
r_scangle_it4.652
r_mcangle_it4.287
r_scbond_it3.234
r_mcbond_it2.987
r_angle_refined_deg1.347
r_nbtor_refined0.309
r_nbd_refined0.183
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.13
r_chiral_restr0.098
r_bond_refined_d0.01
r_gen_planes_refined0.008
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 Atoms2406
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms6

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
PHASERphasing