X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NSXPDB entry '2NSX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52980.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M Hepes pH 7.5, SOAK with 500uM isofagomine for 10 min, glycerol in cryo, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2462.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.311α = 90
b = 92.013β = 111.21
c = 152.362γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.432.12103572

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 DIFFRACTIONTHROUGHOUTPDB entry '2NSX2.432.1298363103572520993.170.1820.1780.245RANDOM27.274
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]
0.2-0.17-0.18-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.898
r_dihedral_angle_4_deg20.705
r_dihedral_angle_3_deg17.889
r_dihedral_angle_1_deg8.265
r_scangle_it3.684
r_scbond_it2.398
r_angle_refined_deg1.957
r_mcangle_it1.659
r_mcbond_it0.978
r_xyhbond_nbd_refined0.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.898
r_dihedral_angle_4_deg20.705
r_dihedral_angle_3_deg17.889
r_dihedral_angle_1_deg8.265
r_scangle_it3.684
r_scbond_it2.398
r_angle_refined_deg1.957
r_mcangle_it1.659
r_mcbond_it0.978
r_xyhbond_nbd_refined0.335
r_nbtor_refined0.313
r_nbd_refined0.229
r_symmetry_vdw_refined0.198
r_symmetry_hbond_refined0.184
r_chiral_restr0.134
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15720
Nucleic Acid Atoms
Solvent Atoms905
Heterogen Atoms426

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction